diff --git a/Image/tree_proof_1.png b/Image/tree_proof_1.png new file mode 100644 index 00000000..629deeec Binary files /dev/null and b/Image/tree_proof_1.png differ diff --git a/Project-1/Peihong_Xie_Project_1_50375781.md b/Project-1/Peihong_Xie_Project_1_50375781.md new file mode 100644 index 00000000..1cc96247 --- /dev/null +++ b/Project-1/Peihong_Xie_Project_1_50375781.md @@ -0,0 +1,302 @@ +# Project 1 Assignment + +Your first 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. + +```Tip #1: Carefully study the Hedman selections assigned, as several of the questions are taken directly from the textbook. +Tip #2: Google is your friend. An important skill to pick up in this class is recognizing when to think hard and when to think smart. You might find answers to some of the questions below simply by googling; you might find pieces of answers to parts of some question below, which will need to be combined; then again, you might not find any help at all because the questions are more novel than they initially appear. I encourage you to use existing resources as guidance, but be careful. My reputation for asking students tricky questions is well-earned. +Tip #3: Work _together_ to solve these problems, even for initial submissions and when you do, document this in github. For example, you might feel like you nearly have answers to question 1, but would love another pair of eyes. You can then open a post in your local github account, and tag folks from class requesting they check out your work. +Tip #4: The work we do is challenging; that should be assumed. You are smart enough to be here; that should also be assumed. We have neither time nor space for shaming, but all of time and space for praising. Be cognizant of how your messages might be received, and err on the side of caution. It is hard to surmise intent from text alone. For my part, I treat text only communications the way modern musicals are written: Little subtext; emotions on the sleeve. +``` + + +Note: The standard interpretation of the logical symbols - "∨", "∧", "→", "¬", "∀", "∃" - is assumed throughout. + + +[1] Provide the truth tables for each of the following propositional logic formulas. State whether each is a tautology, a contradiction, or contingent: + ```(a) (¬A→B)∨((A∧¬C)→B) + (b) (A→B)∧(A→¬B) + (c) (A→(B∨C))∨(C→¬A) + (d) ((A→B)∧C)∨(A∧D) +``` + +Answer: + +(a) Tautology +| A | B | C | ¬A→B | A∧¬C | (A∧¬C)→B | (¬A→B)∨((A∧¬C)→B) | +| --- | --- | --- | --- | --- | --- | --- | +| 1 | 1 | 1 | 1 | 0 | 1 | 1 | +| 1 | 1 | 0 | 1 | 1 | 1 | 1 | +| 1 | 0 | 1 | 1 | 0 | 1 | 1 | +| 0 | 1 | 1 | 1 | 0 | 1 | 1 | +| 1 | 0 | 0 | 1 | 1 | 0 | 1 | +| 0 | 1 | 0 | 1 | 0 | 1 | 1 | +| 0 | 0 | 1 | 0 | 0 | 1 | 1 | +| 0 | 0 | 0 | 0 | 0 | 1 | 1 | + +(b) Contingent +| A | B | A→B | A→¬B | (A→B)∧(A→¬B) | +| --- | --- | --- | --- | --- | +| 1 | 1 | 1 | 0 | 0 | +| 1 | 0 | 0 | 1 | 0 | +| 0 | 1 | 1 | 1 | 1 | +| 0 | 0 | 1 | 1 | 1 | + +(c) Tautology +| A | B | C | B∨C | A→(B∨C) | C→¬A | (A→(B∨C))∨(C→¬A)) | +| --- | --- | --- | --- | --- | --- | --- | +| 1 | 1 | 1 | 1 | 1 | 0 | 1 | +| 1 | 1 | 0 | 1 | 1 | 1 | 1 | +| 1 | 0 | 1 | 1 | 1 | 0 | 1 | +| 0 | 1 | 1 | 1 | 1 | 1 | 1 | +| 1 | 0 | 0 | 0 | 0 | 1 | 1 | +| 0 | 1 | 0 | 1 | 1 | 1 | 1 | +| 0 | 0 | 1 | 1 | 1 | 1 | 1 | +| 0 | 0 | 0 | 0 | 1 | 1 | 1 | + +(d) Contingent +| A | B | C | D | A→B | (A→B)∧C | A∧D | ((A→B)∧C)∨(A∧D) +| --- | --- | --- | --- | --- | --- | --- |--- | +| 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | +| 1 | 1 | 1 | 0 | 1 | 1 | 0 | 1 | +| 1 | 1 | 0 | 1 | 1 | 0 | 1 | 1 | +| 1 | 0 | 1 | 1 | 0 | 0 | 1 | 1 | +| 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | +| 1 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | +| 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | +| 0 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | +| 0 | 1 | 1 | 0 | 1 | 1 | 0 | 1 | +| 0 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | +| 1 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | +| 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | +| 0 | 0 | 1 | 0 | 1 | 1 | 0 | 1 | +| 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | +| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | +| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | + +[2] A _literal_ is an atomic formula or the negation of an atomic formula. We say a formula is in _conjunctive normal form_ (CNF) if it is the conjunction of the disjunction of literals. Find propositional logic formulas in CNF equivalent to each of the following: + ```(a) (A→B)→C + (b) (A→(B∨C))∨(C→¬A) + (c) (¬A∧¬B∧C)∨(¬A∧¬C)∨(B∧C)∨A +``` +Answer: + +(a) CNF: (A∨C)∧(¬B∨C) + +(b) CNF: B∨¬B (the CNF of a tautology is any formula of the form "p∨¬p") + +(c) CNF: B∨¬B (the CNF of a tautology is any formula of the form "p∨¬p") + +[3] Let V be the vocabulary of first-order logic consisting of a binary relation P and a unary relation F. Interpret P(x,y) as “x is a parent of y” and F(x) as “x is female.” Where possible define the following formulas in this vocabulary; where not possible, explain why: + ```(a) B(x,y) that says that x is a brother of y + (b) A(x,y) that says that x is an aunt of y + (c) C(x,y) that says that x and y are cousins + (d) O(x) that says that x is an only child + (e) T(x) that says that x has exactly two brothers +``` + +Answer: + + +(a) B(x,y) $\leftrightarrow$ ∃u(P(u,x)∧P(u,y))∧¬F(x)∧¬(x=y) + +(b) A(x,y) $\leftrightarrow$ ∃u∃w(P(u,y)∧P(w,x)∧P(w,u)∧¬(x=u))∧F(x) + +(c) C(x,y) $\leftrightarrow$ ∃s∃u∃v∃w∃z(P(w,z)∧P(z,x)∧((P(w,u)∧P(u,y))∨(P(s,w)∧P(s,v)∧P(v,u)∧P(u,y)))∧¬(x=y) + +Here consider two situations (by disjunction): + +(i) x's parent z has sibiling u (who has the same parent w as z), and y is u's child and thus x's first cousion. +(ii) x's grandparent w has sibiling v (who has the same parent s as w), and y is a grandchild of v and thus a second cousin of x. + + + +(d) O(x) $\leftrightarrow$ ∃u(P(u,x)∧∀y(P(u,y)→x=y)) + +(e) T(x) $\leftrightarrow$ ∃u∃y∃z(¬(y=z)∧¬(x=y)∧¬(x=z)∧P(u,x)∧P(u,y)∧P(u,z)∧¬F(y)∧¬F(z))∧∀w(P(u,w)∧¬F(w)→ w=x ∨ w=y ∨ w=z) + + + +[4] Let V be a vocabulary of the attribute (concept) language with complements (ALC) consisting of a role name "parent_of" and a concept name "Male". Interpret parent_of as "x is a parent of y" and M as "x is male". Where possible define the following formulas in this vocabulary; where not possible, explain why: + ```(a) B that says that x is a brother of y + (b) A that says that x is an aunt of y + (c) C that says that x and y are cousins + (d) O that says that x is an only child + (e) T that says that x has exactly two brothers +``` + +Answer: + +**Given ALC has no inverse role or numerical restrictions, B, A, C, O, and T cannot be represented here. For example, a brother must be a child of someone, but he might not be a parent of someone (if he is barren). That is, without the inverse role of parent_of, it is impossible to characterize him as a brother only by using parent_of.** + +The following are some definitional attempts within ALCIN. + +**Approach 1 for ALCIN (directly introducing the inverse of a primary role)** + +(a) $B ≡ M\sqcap ∃parentOf^-.(\ge2 parentOf.(M\sqcup ¬M))$ + +(b) $A ≡ ¬M\sqcap ∃parentOf^-.((∃parentOf.(∃parentOf.M\sqcup ¬M))\sqcap \ge2 parentOf.(M\sqcup ¬M))$ + +(c) $C ≡ ∃parentOf^-.(∃parentOf^-.(\ge2parentOf.(∃parentOf.M\sqcup ¬M)))$ + +(d) $O ≡ ∃parentOf^-.(\le1 parentOf.(M\sqcup ¬M))$ + +(e) $T ≡ (M\sqcap ∃parentOf^-.(\le3 parentOf.M \sqcap \ge3 parentOf.M))\sqcup(¬M\sqcap∃parentOf^-.(\le2 parentOf.M \sqcap \ge2 parentOf.M))$ + + +**Approach 2 for ALCIN (indirectly introducing the inverse of a primary role, based on Ali and Giacomo, after my revisions)** + +In fact, these two approaches are interchangable because $parentOf^-$ in my own approach plays the same role as $p1^-$ in my revised Ali and Giacomo's approach: + +(a) B that says that x is a brother of y + + Person ≡ M ⊔ ¬M + + **p2** (parent of at least 2 children) ≡ ≥2 ∃parent_of.Person + + The inverse of p2 means that x is one of at least 2 children produced by y. + + B (brother) ≡ M ⊓ ∃p2¯.Person + +(b) A that says that x is an aunt of y + + A ≡ ¬M ⊓ (∃p2¯.(≥ 2 parent_of. (∃parent_of. Person)) ⊔ ¬∃parent_of. Person) + +(c) C that says that x and y are cousins + + **gp2** (Grandparent with at least two children which each have children) ≡ ≥2 parentof. (∃parentof. Person) + + C ≡ gp2¯. Person + + But this would only describe one of the two cousins, i.e. "being a cousin of someone" or "having a cousin". We cannot define "being cousins" in description logic. + +(d) O that says that x is an only child + + **parent_only** (be a parent of exactly one child) ≡ (≥1 parent_of. Person) ⊓ (≤1 parent_of. Person) + + O ≡ ∃parent_only¯.Person + +(e) T that says that x has exactly two brothers. + + **p3m** (be a parent of exactly three male children) ≡ (≥3 parent_of. Male) ⊓ (≤3 parent_of. Male) + + **p1** (be a parent of at least one child) ≡ ≥1 parent_of. Person -- the inverse of p1 is just "be a child of"! + + T ≡ ∃p3m¯.Person ⊔ (¬M ⊓ ∃p1¯. (≥2 parent_of. Male ⊓ ≤2 parent_of. Male)) + + -- This means, either x is one of exactly 3 boys produced by a person (so x has exactly two brothers), or x is female and is a child of a person who has exactly two boys (so x has also exactly two brothers) + +[5] Select two formulas defined in ALC from question 4 to form the basis of a T-Box. Supplement this T-box with whatever other axioms you like, as well as an A-box, so that you ultimately construct a knowledge base K = (T,A). Provide a _model_ of K. This may be graphical or symbolic or both. + +Answer: + +**There is no formula from Question 4 available here.** + +$K_1 = (T_1,A_1)$ such that: + +T-box $T_1$={GP (grandparent) ≡ ∃parentOf.(∃parentOf.M∪¬M)} + +A-box $A_1$={(Mary,Karl):ParentOf, Karl:Male}. + +The following is a model $\Im=(\bigtriangleup^\Im,.^\Im)$ of $K_1$: + +$\bigtriangleup^\Im$={a,b,c} + +$M^\Im$={a} + +$GP^\Im$={c} + +$parentOf^\Im$={(c,b),(b,a)} + +$Karl^\Im$={a} + +$Mary^\Im$={b} + +$Jack^\Im$={c} + +[6] Explain the difference - using natural language - between the first-order prefixes: + ```(a) ∃x∀y and ∀x∃y + (b) ∃x∀y∃z and ∀x∃y∀z + (c) ∀x∃y∀z∃w and ∃x∀y∃z∀w +``` +Answer: + +(a) ∃x∀y means “there exists x such that for all y” while ∀x∃y means "for all x, there exists y such that" + +(b) ∃x∀y∃z means “there exists x such that for all y, there exists z such that” while ∀x∃y∀z means "for all x, there exists y such that for all z" + +(c) ∀x∃y∀z∃w means "for all x, there exists y such that for all z, there exists w such that" while ∃x∀y∃z∀w means "there exists x such that for all y, there exists z such that for all w" + +[7] Show that the following sentences are not equivalent by exhibiting a graph that models one but not both of these sentences: +``` +∀x∃y∀z(R(x,y) ∧ R(x,z) ∧ R(y,z)) +∃x∀y∃z(R(x,y) ∧ R(x,z) ∧ R(y,z)) +``` + +Answer: + +The following graph models the second sentence but not the first sentence: + +Verticles: a, b, c + +Edges: ab, ac, aa (loop) + +```mermaid +graph LR +A((a)) ---B((b)) +A((a)) ---C((c)) +A((a)) ---A((a)) +``` + +[8] Using an online tableau proof generator - such as the one found here `https://www.umsu.de/trees/` - provide tree proofs of the following entailments, which are known as the De Morgan's laws: +``` +(a) ∀x∀y(¬(Px ∧ Qx) → (¬Px ∨ ¬Qx)) +(b) ∀x∀y(¬(Px ∨ Qx) → (¬Px ∧ ¬Qx)) +(c) ∀x∀y((¬Px ∨ ¬Qx) → ¬(Px ∧ Qx)) +(d) ∀x∀y((¬Px ∧ ¬Qx) → ¬(Px ∨ Qx)) +``` + +Answer: + +(a) + +![picture 1](https://github.com/peihongx/PHI-696/blob/main/Project-1/tree_1.jpg) + +(b)(c) + +![picture 2](https://github.com/peihongx/PHI-696/blob/main/Project-1/tree_2.jpg) + + +(d) + +![picture 3](https://github.com/peihongx/PHI-696/blob/main/Project-1/tree_3.jpg) + + +[9] Using a natural deduction proof generator - such as the one found here `https://proofs.openlogicproject.org/` - provide natural deduction proofs for each of De Morgan's laws. + +Answer: + +(a) + +![picture 1](https://github.com/peihongx/PHI-696/blob/main/Project-1/fitch_proof_1.PNG) + +(b) + +![picture 1](https://github.com/peihongx/PHI-696/blob/main/Project-1/fitch_proof_2.PNG) + +(c) + +![picture 1](https://github.com/peihongx/PHI-696/blob/main/Project-1/fitch_proof_3.PNG) + +(d) + +![picture 1](https://github.com/peihongx/PHI-696/blob/main/Project-1/fitch_proof_4.PNG) + +[10] Compare and contrast the proofs provided for (a) in your answers to questions 8 and 9. Explain the different assumptions, strategies, etc. exhibited in tree proofs vs natural deduction proofs. + +Answer: + +For (a), a Fitch-style natural deduction proof relies on deductive rules like disjunction elimination or double negation elimination (DNE) to a more substantive degree than a tree proof. + +While a Fitch-style natural deduction proof is a **combinational application of different means of derivation**, a tree proof is essentially **an application of indirect derivation**. That is, when we do a tree proof, we have to decompose the target (complex) formula into its subformulas, and then differently connect negations of those subformulas in order to form different paths. Once when all paths somehow involve a contradiction, then the opposite possibilities of the target formula are all shown to be implausible, and thus the target formula will be proved. + +Moreover, a Fitch-style natural deduction proof is to apply rules to the target formula and its logical consequents, while a tree proof does not apply the same rules but concentrates on finding possible logical contradictions among negated subformulas of the target formula. diff --git a/Project-1/README.md b/Project-1/README.md index 060b7b12..ed77a085 100644 --- a/Project-1/README.md +++ b/Project-1/README.md @@ -73,3 +73,4 @@ Note: The standard interpretation of the logical symbols - "∨", "∧", "→", 10. Compare and contrast the proofs provided for (a) in your answers to questions 8 and 9. Explain the different assumptions, strategies, etc. exhibited in tree proofs vs natural deduction proofs. + diff --git a/Project-1/fitch_proof_1.PNG b/Project-1/fitch_proof_1.PNG new file mode 100644 index 00000000..77463abc Binary files /dev/null and b/Project-1/fitch_proof_1.PNG differ diff --git a/Project-1/fitch_proof_2.PNG b/Project-1/fitch_proof_2.PNG new file mode 100644 index 00000000..6c2630c8 Binary files /dev/null and b/Project-1/fitch_proof_2.PNG differ diff --git a/Project-1/fitch_proof_3.PNG b/Project-1/fitch_proof_3.PNG new file mode 100644 index 00000000..44b6794f Binary files /dev/null and b/Project-1/fitch_proof_3.PNG differ diff --git a/Project-1/fitch_proof_4.PNG b/Project-1/fitch_proof_4.PNG new file mode 100644 index 00000000..375557fc Binary files /dev/null and b/Project-1/fitch_proof_4.PNG differ diff --git a/Project-1/tree_1.jpg b/Project-1/tree_1.jpg new file mode 100644 index 00000000..69a0e7f3 Binary files /dev/null and b/Project-1/tree_1.jpg differ diff --git a/Project-1/tree_2.jpg b/Project-1/tree_2.jpg new file mode 100644 index 00000000..5f2a9067 Binary files /dev/null and b/Project-1/tree_2.jpg differ diff --git a/Project-1/tree_3.jpg b/Project-1/tree_3.jpg new file mode 100644 index 00000000..cba42785 Binary files /dev/null and b/Project-1/tree_3.jpg differ diff --git a/Project-1/tree_proof_1.png b/Project-1/tree_proof_1.png new file mode 100644 index 00000000..629deeec Binary files /dev/null and b/Project-1/tree_proof_1.png differ diff --git a/Project-1/tree_proof_2.png b/Project-1/tree_proof_2.png new file mode 100644 index 00000000..c03e3aaf Binary files /dev/null and b/Project-1/tree_proof_2.png differ diff --git a/Project-1/tree_proof_3.png b/Project-1/tree_proof_3.png new file mode 100644 index 00000000..64b07615 Binary files /dev/null and b/Project-1/tree_proof_3.png differ diff --git a/Project-1/tree_proof_4.png b/Project-1/tree_proof_4.png new file mode 100644 index 00000000..14cd833f Binary files /dev/null and b/Project-1/tree_proof_4.png differ diff --git a/Project-2/Mereology Project 2.owl b/Project-2/Mereology Project 2.owl new file mode 100644 index 00000000..148af9c7 --- /dev/null +++ b/Project-2/Mereology Project 2.owl @@ -0,0 +1,290 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #D + karlx + + + + #D + is_disjoint_with + + + + #O + karlx + + + + #O + overlaps + + + + #P + karlx + + + + #P + part_of + + + + #PP + karlx + + + + #PP + proper_part_of + + + + #a + karlx + + + + #alternative_label + karlx + + + + #alternative_label + 2023-02-18T17:38:19Z + + + + #b + karlx + + + + #c + karlx + + + + #e + karlx + + + + #e + 2023-02-20T05:34:49Z + + + + #editor_note + karlx + + + + #editor_note + 2023-02-18T17:41:09Z + + + + #f + karlx + + + + #f + 2023-02-20T05:35:02Z + + + + #g + karlx + + + + #g + 2023-02-20T05:35:14Z + + + + #iP + karlx + + + + #iP + has_part + + + + #iPP + karlx + + + + #iPP + has_proper_part + + + + + + + diff --git a/Project-2/Mereology Project 2.properties b/Project-2/Mereology Project 2.properties new file mode 100644 index 00000000..8bae5bcb --- /dev/null +++ b/Project-2/Mereology Project 2.properties @@ -0,0 +1,5 @@ +#Sat Feb 25 19:00:29 EST 2023 +jdbc.url= +jdbc.driver= +jdbc.user= +jdbc.password= diff --git a/Project-2/Peihong_Xie_Project_2_50375781.md b/Project-2/Peihong_Xie_Project_2_50375781.md new file mode 100644 index 00000000..58c74dde --- /dev/null +++ b/Project-2/Peihong_Xie_Project_2_50375781.md @@ -0,0 +1,319 @@ +# Karl Project 2 + +Your second 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. + +``` +Tip #1: Carefully study the Baader, et. al. selections assigned on bisimulation; it is deceptively subtle, and quite powerful. +Tip #2: Google is still your friend. So is stackexchange... +Tip #3: Work together to solve these problems, even for initial submissions and when you do, document this in github. +Tip #4: Work together as a team. +``` + +**[1]** Let V be a vocabulary of ALCI consisting of a role name "P". Interpret part_of as "x is a part of y". Using this role name, define the following formulas in this language: +``` + (a) PP that says that x is a proper part of y + (b) iPP that says that y is a proper part of x + (c) iP that says that x has y as part + (d) O that says that x overlaps y + (e) D that says that x and y are disjoint +``` + +Answer: + +(a) $PP ≡ P\sqcap ¬P^-$ + +(b) $iPP ≡ P^-\sqcap ¬P$ + +(c) $iP ≡ P^-$ + +(d) $O ≡ ∃P^-.(∃P.\top)$ + +(e) $D ≡ ∀P^-.(∀P.\bot)$ + +**[2]** Use your axioms from question 1 as the basis of an ALCI T-Box. Supplement this T-box with whatever other axioms you like, as well as an A-box, so that you ultimately construct a knowledge base K = (T,A). Provide a _model_ of K. This may be graphical or symbolic or both. + +Answer: + +K = (T,A) such that + +T={PP ≡ P ⊔ ¬P-, + +$iPP ≡ P^-\sqcap ¬P$, + +$iP ≡ P^-$, + +$O ≡ ∃P^-.(∃P.\top)$, + +$D ≡ ∀P^-.(∀P.\bot)$, + +$TP (partOfPartof) ≡ P.(P)$, + +$SI (selfIdenticalTo) ≡ P\sqcap P^-$} + +A={(Handle,Door):P, (Karl,Mary):D, (Karlhead,Karl):P, (Maryhand,Mary):P} + + +The following is a model $\Im=(\bigtriangleup^\Im,.^\Im)$ of K: + +$\bigtriangleup^\Im$={a,b,c,d,e,f} + +$P^\Im$={(a,b), (e,c), (f,d),(a,a),(b,b),(c,c),(d,d),(e,e),(f,f)} + +$P¯^\Im$={(b,a), (c,e), (d,f),(a,a),(b,b),(c,c),(d,d),(e,e),(f,f)} + +$PP^\Im$={(a,b), (e,c), (f,d)} + +$iPP^\Im$={(b,a), (c,e), (d,f)} + +$iP^\Im$={(b,a), (c,e), (d,f),(a,a),(b,b),(c,c),(d,d),(e,e),(f,f)} + +$O^\Im$={(a,b), (e,c), (f,d),(b,a), (c,e), (d,f)} + +$D^\Im$={(c,d), (d,c), (b,c), (c,b), (b,d), (d,b), (a,e),(e,a),(a,f),(f,a),(e,f),(f,e),(a,c),(c,a),(a,d),(d,a),(b,e),(e,b),(d,e),(e,d),(b,f),(f,b),(c,f),(f,c)} + +$TP^\Im$=$\emptyset$ + +$SI^\Im$={(a,a),(b,b),(c,c),(d,d),(e,e),(f,f)} + + +$Handle^\Im$={a} + +$Door^\Im$={b} + +$Karl^\Im$={c} + +$Mary^\Im$={d} + +$Karlhead^\Im$={e} + +$Maryhand^\Im$={f} + + +This model seems very complex at first glance, but it is actually intuitive: Imagine two persons Karl and Mary, and a door called "Door". Karl has a head called "Karlhead", Mary has a hand called "Maryhand", and Door has a handle called "Handle". My model is designed to describe in detail mereological relations between them. + +```mermaid +classDiagram +class Door + Door : Handle + +class Karl + Karl : Karlhead + +class Mary + Mary : Maryhand +``` + +**[3]** Translate the following first-order logic axioms into ALCI: +``` +(a) ∀x∃y∀z(R(x,y) ∧ R(x,z) ∧ R(y,z)) +(b) ∃x∀y∃z(R(x,y) ∧ R(x,z) ∧ R(y,z)) +(c) ∀y(R(x, y) → ∃x(R(y, x) ∧ ∀y(R(x, y) → A(y)))) +(d) (∀y)(R(x, y) → A(y)) ∧ (∃y)(R(x, y) ∧ B(y)) +``` + +Answer: + +(a) $∃R.(∀R.(∀R¯.\top))$ + +Fixing x (restricted by an impicit universal quantifer), this formula says: All x is R-related to some y such that y is R-related to all z such that z is R¯-related to all x (or, all x is R-related to z). + +(b) $∃R^-.(∃R.(∀R^-.\top))$ + +Fixing y (restricted by an impicit universal quantifer), this formula says: All y is is R¯-related to some x (or, some x is R-related to y) such that x is R-related to some z such that z is R¯-related to all y (or, all y is R-related to z). + +(c) $∀R.(∃R.(∀R.A))$ + +(d) $∀R.A\sqcap∃R.B$ + +**[4]** Provide an interpretation I1 for ALC and an interpretation I2 for ALCN - each distinct from any interpretation covered in class so far - and construct a bisimulation that demonstrates ALCN is more expressive than ALC. Use the [mermaid syntax](https://github.com/mermaid-js/mermaid) of markdown to provide a graphical representation of your work. Feel free to use the [mermaid live editor](https://mermaid.live/) when diagramming. + +Answer: + +Let $I_1=(\bigtriangleup^1,.^1)$ is an interpretation for ALC such that: + +$\bigtriangleup$I1={a1,b1,c1} + +parentOfI1 = {(a1,b1),(b1,c1)} + +```mermaid +graph TD +A((a1)) -->|parentOf|B((b1)) +B((b1)) -->|parentOf|C((c1)) +``` + +Let $I_2=(\bigtriangleup^2,.^2)$ is an interpretation for ALCN such that: + +$\bigtriangleup$I2={a2,b2,c2,d2,e2,f2,g2,h2,m2,n2} + +parentOfI1 = {(a2,b2),(a2,c2),(a2,d2),(b2,e2),(b2,f2),(c2,g2),(c2,h2),(d2,m2),(d2,n2)} + +```mermaid +graph TD +A((a2)) -->|parentOf|B((b2)) +A((a2)) -->|parentOf|C((c2)) +A((a2)) -->|parentOf|D((d2)) +B((b2)) -->|parentOf|E((e2)) +B((b2)) -->|parentOf|F((f2)) +C((c2)) -->|parentOf|G((g2)) +C((c2)) -->|parentOf|H((h2)) +D((d2)) -->|parentOf|M((m2)) +D((d2)) -->|parentOf|N((n2)) +``` + +It is clear that $p$ = {(a1,a2),(b1,b2),(b1,c2),(b1,d2),(c1,e2),(c1,f2),(c1,g2),(c1,h2),(c1,m2),(c1,n2)} is a bisimulation between $I_1$ and $I_2$, so we have ($I_1$, a1)~($I_2$, a2). However, $a2\in(\ge3 parentOf.(\ge2 parentOf))$I2, but $a1\notin(\ge3 parentOf.(\ge2 parentOf))$I1, so $(\ge3 parentOf.(\ge2 parentOf))$ is not a ALC concept (otherwise it should be the case that $a1\in(\ge3 parentOf.(\ge2 parentOf))$I1). Therefore, we find that a ALCN concept which is not ALC concept, showing that ALCN is more expressive than ALC. + +**[5]** Provide an interpretation I1 for ALC and an interpretation I2 for ALCN - each distinct from any interpretation covered in class so far - and construct a bisimulation that _does not_ demonstrate ALCN is more expressive than ALC. Use the [mermaid syntax](https://github.com/mermaid-js/mermaid) of markdown to provide a graphical representation of your work. Feel free to use the [mermaid live editor](https://mermaid.live/) when diagramming. + +Answer: + +Let $I_1=(\bigtriangleup^1,.^1)$ is an interpretation for ALC such that: + +$\bigtriangleup$I1={a1,b1,c1,d1,e1} + +rI1 = {(a1,b1),(a1,c1),(a1,d1),(a1,e1)} + +```mermaid +graph TD +A((a1)) -->|r|B((b1)) +A((a1)) -->|r|C((c1)) +A((a1)) -->|r|D((d1)) +A((a1)) -->|r|E((e1)) +``` + +Let $I_2=(\bigtriangleup^2,.^2)$ is an interpretation for ALCN such that: + +$\bigtriangleup$I1={a2,b2,c2,d2,e2,f2,g2,h2,m2,n2} + +rI1 = {(a2,b2),(a2,c2),(a2,d2),(a2,e2),(f2,g2),(f2,h2),(f2,m2),(f2,n2)} + +```mermaid +graph TD +A((a2)) -->|r|B((b2)) +A((a2)) -->|r|C((c2)) +A((a2)) -->|r|D((d2)) +A((a2)) -->|r|E((e2)) +F((f2)) -->|r|G((g2)) +F((f2)) -->|r|H((h2)) +F((f2)) -->|r|M((m2)) +F((f2)) -->|r|N((n2)) +``` + +It is clear that $p$ = {(a1,a2),(b1,b2),(c1,c2),(d1,d2),(e1,e2),(a1,f2),(b1,g2),(c1,h2),(d1,m2),(e1,n2)} is a bisimulation between $I_1$ and $I_2$. But $I_1$ and $I_2$ _does not_ demonstrate ALCN is more expressive than ALC because these two interpretations are isomorphic. + + +**[6]** Explain the difference - using natural language - between the description logic expressions: + ``` + (a) ∃r.C and ∀r.C + (b) ∃r-.C and ∀r-.C + (c) <=nr and <=nr.C + (d) ∃r-.C and ∃r-.{a} +``` + +Answer: + +(a) ∃r.C means that x has a r-filler which is an instance of C; and ∀r.C means that x's all r-fillers are instances of C. + +(b) ∃r-.C means that x has a r-predecessor which is an instance of C; and ∀r-.C means x's all r-predecessors are instances of C. + +(c) <=nr means that x has at most $n$ r-fillers; and <=nr.C means that x has at most $n$ r-fillers instantiating C. + +(d) ∃r-.C means that x has a r-predecessor which is an instance of C; and ∃r-.{a} means that x has a r-predecessor which is $a$. + +**[7]** There is a delightfully helpful subreddit called "ELI5" which stands for something like "explain it like I'm 5" where users post conceptually challenging questions and other users attempt to provide explanations in simple, jargon-free, terms that presumably a 5 year-old could understand. Using this as a model, explain the _finite model property_. Be sure to provide a simple example and explain when the property might be important, and when it is not so important. + +Answer: + +(1) When we say that a concept like "Dog" is satisfiable in a description logic, we mean that there is a model to assign some individual dogs to it. Now if every satisfiable concept in that description logic has a finite model, a model which has only finitely many elements, then we say that logic has _finite model property_. + +(2) Example: Consider a simple _ALC_ T-box T1={$Dog\sqsubseteq Mammal$, $Person\equiv Rational\sqcap Mammal$}. The _ALC_ concept $Spider$ is satisfiable with respect to T1, and it is not difficult to find that $Spider$ has a finite model with respect to T1. For example, $I_1=(\bigtriangleup^1,.^1)$ such that: + +$\bigtriangleup^1$={a,b,c,d} + +$Dog^1$ = {b,c} + +$Mammal^1$ = {a,b,c} + +$Person^1$= {a} + +$Rational^1$= {a} + +$Spider^1$= {d} + +It is clear that $I_1$ is a model of T1, and $Spider$ has an instance _d_ in $I_1$. So $I_1$ is a finite model of $Spider$ with respect to T1. + +(3) Finite model property (FMP) of a description logic is very important if we wanna design a decidable algorithm for the satisfiability of its concepts, and thus determine a conceptual hierarchy of that logic. But if we want a more expressive description logic like _ALCIN_, then FMP can be sacrified for its expressive power. Also, sometimes we are required to check the consistency of some knowledge base. In that case, FMP is not very useful because that knowledge base may not have a finite model. + +**[8]** Following up on the preceding , explain the _tree model property_. Be sure to provide a simple example and explain when the property might be important, and when it is not so important. + +Answer: + +(1) When we say that a concept like "Father" is satisfiable in a description logic, we mean that there is a model to assign some individual men to it. Now if every satisfiable concept in that description logic has a tree model, then we say that logic has _tree model property_. Here a model is a _tree model_ if it can be represented as a tree-like graph, which has only one root, viz. a node without parent, and every child node below the root has only one parent. + +(2) Consider a simple _ALC_ T-box T2={$Daughter\sqsubseteq Female$, $Son \sqsubseteq Male$}. The _ALC_ concept $Father$ is satisfiable with respect to T2, and it is not difficult to find that $Father$ has a tree model with respect to T2. For example, $I_2=(\bigtriangleup^2,.^2)$ such that: + +$\bigtriangleup^2$={Karl,Mary,Jack,Lucy} + +$Daughter^2$ = {Mary,Lucy} + +$Female^2$ = {Mary,Lucy} + +$Son^2$= {Jack} + +$Male^2$= {Karl,Jack} + +$Father^2$= {Karl} + +$parentOf^2$ = {(Karl,Mary),(Karl,Jack),(Karl,Lucy)} + +```mermaid +graph TD +A((Karl)) -->|parentOf|B((Mary)) +A((Karl)) -->|parentOf|C((Jack)) +A((Karl)) -->|parentOf|D((Lucy)) +``` +It is clear that $I_2$ is a model of T2, and $Father$ has an instance _Karl_ in $I_2$. And $I_2$ is a tree model of $Father$ with respect to T2. + +(3) TMP is crucial to tableau-based algorithms for the consistency check of knowledge base and applied ontology. Most of applied ontologies, especially those BFO-based ones, have TMP, allowing that their consistency can be checked by tableau reasonings. Moreover, TMP can show decidability of satisfiability of ALC concepts in the so-called automata-based approach. + +However, if we deal with linear roles or small datasets, TMP might not be very useful because its poor generalization performance in these cases. + +**[9]** Open the Protege editor and create object properties for each of the role names that you constructed in question 1. You should have at least 6 object properties. Assert in the editor that P is a sub-property of O, that P is transitive, and that O is symmetric. Next, add individuals - a, b, c - to the file and assert that c is part of a and that c overlaps b. Running the reasoner should reveal - highlighted in yellow if you select the individual c - that c overlaps a. Using the discussion in the selections from chapter 4 of the Baader, et. al. text as a guide, explain how the tableau algorithm is generating this inference. Also, provide a screenshot of the results of your reasoner run with c highlighted. + +Answer: + +![picture 1](https://github.com/peihongx/PHI-696/blob/main/Project-2/pic_1_1.PNG) + +![picture 1](https://github.com/peihongx/PHI-696/blob/main/Project-2/pic_1_2.PNG) + +![picture 1](https://github.com/peihongx/PHI-696/blob/main/Project-2/pic_1_3.PNG) + + +The tableau algorithm generates this inference (c,a):O in such a way: + +From Theorem 2.17 (Baader.etc: 32), we have $(\emptyset,A)\models(c,a):O$ iff ($\emptyset,A\cup$ {(c,a):¬O}) _is_ not consistent. Here A={(c,a):P,(c,b):O}. + +Therefore, the target inference problem becomes the problem of determining that the new A-box A*={(c,a):P,(c,b):O, (c,a)¬O} is inconsistent. + +In order to calculate with the inconsistency problem, the algorithm _expand_ will first apply concept expansion rules to A* to construct a complete A-box. However, as we notice, A* does not include any concept, so the application of expansion rules to A* is empty. + +However, by the fact that P is a sub-property of O and that (c,a):P, the algorithm _expand_ infers that (c,a):O, and thus finds that A* implies a clash {(c,a):O, (c,a):¬O}. Thus, $expand(A^*)= \emptyset$. + +In light of this, a larger alrorithm _consistent_ which includes the algorithm _expand_ will return "inconsistent". Given Theorem 2.17, we have shown that $(\emptyset,A)\models(c,a):O$. + +**[10]** Following up on your work in question 9, adjust/add/remove/etc. object properties and individuals in your Protege file so that when you run a reasoner in Protege, you return the following consequences: +``` + (a) a is a proper part of b and disjoint from e + (b) a overlaps c + (c) a is part of b, b is part of f, and a is part of f + (e) There are no parts between a and g in common +``` + +Provide a screenshot of your results here. + +Answers: + +![picture 2](https://github.com/peihongx/PHI-696/blob/main/Project-2/pic_2_1.PNG) + +![picture 3](https://github.com/peihongx/PHI-696/blob/peihong_karl_project_2/Project-2/pic_2_2_1.PNG) + +![picture 4](https://github.com/peihongx/PHI-696/blob/peihong_karl_project_2/Project-2/pic_2_3_1.PNG) diff --git a/Project-2/README.md b/Project-2/README.md index 73dacdc3..a943bd20 100644 --- a/Project-2/README.md +++ b/Project-2/README.md @@ -13,7 +13,7 @@ Tip #4: Work together as a team. ``` (a) PP that says that x is a proper part of y (b) iPP that says that y is a proper part of x - (c) iP that says that y has x as part + (c) iP that says that x has y as part (d) O that says that x overlaps y (e) D that says that x and y are disjoint ``` diff --git a/Project-2/pic_1_1.PNG b/Project-2/pic_1_1.PNG new file mode 100644 index 00000000..b62a5bc6 Binary files /dev/null and b/Project-2/pic_1_1.PNG differ diff --git a/Project-2/pic_1_2.PNG b/Project-2/pic_1_2.PNG new file mode 100644 index 00000000..486d1c0d Binary files /dev/null and b/Project-2/pic_1_2.PNG differ diff --git a/Project-2/pic_1_3.PNG b/Project-2/pic_1_3.PNG new file mode 100644 index 00000000..d55be2e0 Binary files /dev/null and b/Project-2/pic_1_3.PNG differ diff --git a/Project-2/pic_2_1.PNG b/Project-2/pic_2_1.PNG new file mode 100644 index 00000000..0f2a3427 Binary files /dev/null and b/Project-2/pic_2_1.PNG differ diff --git a/Project-2/pic_2_2_1.PNG b/Project-2/pic_2_2_1.PNG new file mode 100644 index 00000000..f9d25ad9 Binary files /dev/null and b/Project-2/pic_2_2_1.PNG differ diff --git a/Project-2/pic_2_3_1.PNG b/Project-2/pic_2_3_1.PNG new file mode 100644 index 00000000..b1d04618 Binary files /dev/null and b/Project-2/pic_2_3_1.PNG differ diff --git a/Project-3/Peihong_Xie_Project_3_50375781.md b/Project-3/Peihong_Xie_Project_3_50375781.md new file mode 100644 index 00000000..545389b8 --- /dev/null +++ b/Project-3/Peihong_Xie_Project_3_50375781.md @@ -0,0 +1,381 @@ +# Karl 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 Basic Formal Ontology (https://raw.githubusercontent.com/BFO-ontology/BFO/v2019-08-26/bfo_classes_only.owl) and 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. +``` + (a) Reflexive + (b) Transitive + (c) Symmetric + (d) Functional + (e) Symmetric and Reflexive +``` + +**Answer:** + +(a) Object properties **"simultaneous with", "has part", "part of", "overlaps" and so on** should be reflexive, though it is not listed as so. For example, an event can be simultaneous with itself; also, an entity has_part, part_of, or overlaps itself because it is equivalent to itself. + +(b) The object property **"determined by"** should be transitive, though it is not listed as so. That is, if A is determined by B, and B is determined by C, then A should be determined by C. For example, a small-size ecological cycle is determined by a biological host, say, a human being, that is, as a system at another level of granularity, is determined by his brain. In this case, we can say that the ecological cycle is determined by the human being's brain because its proper functioning leads the human to make efforts in maintaining that cycle. + +(c) The object property **"biotically interacts with"** should be symmetric, though it is not listed as so. If an organism A biotically interacts with another organism B, then it is clear that B is also biotically interacts with A. + +Similarly, **"participates in a biotic-biotic interaction with", "ecologically co-occurs with", "partially overlap" and so on** should also be symmetric. + +(d) The object property **"has skeleton"** should be functional, though it is not listed as so. According to its definition, "has skeleton" is a relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. Given that the maximal subdivision of material entities for any organism has only one, this object property is thereby functional. + +(e) The object property **"overlaps"** should be both symmetric and reflexive, though it is not listed as so. First, if A overlaps B, then A and B has some common part. So B and A has also some common part, and thus B overlaps A. That is, overlapping is symmetric. Second, an entity can overlap itself because it clearly has the same parts with itself. Therefore, overlapping is also reflexive. + +Similarly, **"spatially coextensive with" and "simultaneous with"** is also symmetric and reflexive. + +**[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. +``` + (a) Irreflexive + (b) Transitive + (c) Asymmetric + (d) Functional + (e) Inverse Functional +``` + +**Answer:** + +(a) Although **"has substance added"** is listed as irreflexive, but it should not be so. That is, in some cases, a physical entity can have itself as substance added to it. For example, a portion of water can be added to itself at some time. Similarly, **"has substance removed"** should not be irreflexive, either because we can always remove the same amount of water from itself. + +(b) Although **"aligned with"** is listed as transitive, but it should not be so. Suppose that we have three different quadrilateral objects A, B, and C. A is aligned with B because of their alighed long sides, and B is aligned with C because of their aligned short sides, but A is not thus aligned with C because neither their long nor short sides are not aligned with each other. + +Another funny example: Although **"end after"** is listed as transitive, but it should not be so. A possible counterexample can be found in a spacetime circle: The event of Jack's killing his grandfather ends after the event of his shooting, and the latter ends after the event of his returning to the past. However, the event of Jack's killing his grandfather does not end after the event of his returning to the past. Similarly, **"before"** should not be transitive, either. *(paradox of time travel)* + +(c) Although **"has role in modeling" (or "is used to study")** is listed as asymmetric, but it should not be so. Suppose we wanna study the relation between a biological organism, say, a dog, and its biological niche. Given the mutual dependence between them in some plausible sense, it seems that the dog has role in modeling its niche, but its niche has also role in modeling it. + +(d) Although **"phenotype of"** is listed as functional, but it should not be so. When we say an object property between a subject and an object is functional, we mean that a subject is related to only one object via that property. However, it seems that a particular skin color can be a phenotype of more than one human beings, so "phenotype of" is not functional. + +(e) Although **"has characteristic"** is listed as inverse functional, but it should not be so. When we say an object property between a subject and an object is inverse functional, we mean that an object is related to only one subject via that property. Indeed, only an entity has_characteristic some trope property (e.g., this redness). However, it seems that multiple entities of the same type (e.g. apples) can all have_characteristic some universal (e.g. redness). So "has characteristic" should not be inverse functional if it applies to universals. + +**[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. + (b) Every liver has some cell as part at all times it exists. + (c) John was a child, then an adult, then a senior. + (d) Goofus and Gallant are married at each point in a three year span. +``` + +**Answer:** + +(a) Sally instance_of Object + +Arm is_a Fiat object part + +Tuesday/Wednesday is_a One-dimensional temporal region + +"having some Arm on some Tuesday" instance_of occurrent + +"having no Arm on some Wednesday" instance_of occurrent + +**Result**: "Sally participates in having some Arm on some Tuesday" precedes "Sally participates in having no Arm on some Wednesday". + +Note: "Sally does not have an arm" is ambiguous because it can also be read as "Sally loses an arm but has still other arms" (Maybe Sally is an octopus). + +(b) Liver is_a fiat object part + +Cell is_a material entity + +**Result**: Liver has_part_at_all_times Cell. + +Note: **"has_part_at_all_times"** has been used by Professor Barry Smith to deal with similar cases. + +(c) Childhood is_a Occurrent + +John's childhood instance_of Childhood + +Adulthood is_a Occurrent + +John's adulthood instance_of Adulthood + +Seniorhood is_a Occurrent + +John's seniorhood instance_of Seniorhood + +John instance_of Object + +**Result**: John participates_in John's childhood, and John participates_in John's adulthood, and John participates_in John's seniorhood, and John's childhood precedes John's adulthood, and John's adulthood precedes John's seniorhood. + +(d) t instance_of Zero-dimensional temporal region + +"This three years" instance_of One-dimensional temporal region + +Goofus instance_of Object + +Gallant instance_of Object + +Marriage is_a Occurrent + +**Result**: If any t part_of this three years, then Goofus participates_in some Marriage at t, and Gallant also participates_in some Marriage t. + +Note: Goofus and Gallant might not be a couple. + +**[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. + (b) Every liver has some cell as part at all times it exists. + (c) John was a child, then an adult, then a senior. + (d) Goofus and Gallant have been married for three years; for each day of that span, it is true to assert they are married. +``` + +**Answer:** + +(a) Use the following key: + +Has(x,y,t) : x has y at time t + +Arm (x) : x is an arm + +T(t) : t is a Tuesday + +W(t) : t is a Wednesday + +**s** : Sally + +So the sentence (a) is symbolized as: **∃t∃x(Has(s,x,t) ∧ Arm(x) ∧ T(t)) ∧ ∃t∀x(W(t) ∧ (Arm (x) → ~Has(s,x,t)))** + +(b) Use the following key: + +L(x): x is a liver + +C(x) : x is a cell + +P(x,t): x is present at time t + +Has_Part (x, y, t): x has y as part at time t + +So the sentence (b) is symbolized as: **∀x∀t(L(x) ∧ P(x,t) → ∃y(C(y) ∧ P (y, t) ∧ Has_Part (x,y,t)))** + +(c) Use the following key: + +C(x,t) : x is a child at time t + +A(x,t) : x is an adult at time t + +S(x,t) : x is a senior at time t + +E(t,t'): the time t is wholly earlier than the time t' + +**b** : John + +So the sentence (c) is symbolized as: **∃t∃t'∃t''(C(b,t) ∧ A(b,t') ∧ S(b,t'') ∧ E(t,t') ∧ E(t',t''))** + +(d) Goofus and Gallant have been married for three years; for each day of that span, it is true to assert they are married. + +Use the following key: + +ST(t) : t belongs to this three-year span + +E(x,y) : the time x is wholly earlier than the time y + +D(t) : t is a day + +M (x,t) : x is married at time t + +**a** : Goofus + +**b** : Gallant + +So the sentence (d) is symbolized as: **∀t(D(t) ∧ ST(t) → M(a,t) ∧ M(b,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. + +**Answer:** + +```mermaid +graph LR +A(RDF File Content) -->|is_a|B(Generically Dependent Continuant) +D(Turtle seriaization) -->|is_a|B(Generically Dependent Continuant) +E(XML seriaization) -->|is_a|B(Generically Dependent Continuant) +A(RDF File Content) -->|has_model|D(Turtle seriaization) +A(RDF File Content) -->|has_model|E(XML seriaization) +F(Network) -->|is_a|G(Object Aggregate) +H(Computer) -->|is_a|I(Object) +J(computer 1) -->|instance_of|H(Computer) +K(computer 2) -->|instance_of|H(Computer) +L(computer 3) -->|instance_of|H(Computer) +H(Computer) -->|part_of|F(Network) +H(Computer) -->|is_carrier_of|A(RDF File Content) +H(Computer) -->|is_carrier_of|D(Turtle seriaization) +H(Computer) -->|is_carrier_of|E(XML seriaization) +J(computer 1) -->|enables|M(Data Transmission) +M(Data Transmission) -->|ends_with|N(Data Reception) +K(computer 2) -->|participates_in|N(Data Reception) +L(computer 3) -->|participates_in|N(Data Reception) +O(network I) -->|instance_of|F(Network) +J(computer 1) -->|part_of|O(network I) +K(computer 2) -->|part_of|O(network I) +L(computer 3) -->|part_of|O(network I) +``` + +This graph represents the following key relations: + +– RDF File Content, Turtle and XML are all generically dependent continuants. RDF File Content *has_model* in Turtle and XML. And they are all *carried by* Computer. + +– Computer 1 *enables* the process of Data Transmission, which *ends_with* another process, Data Reception, which has computers 2 and 3 as *participants*. So this part is intended to show that there is some data (Turtle and XML) which are sent from Computers 1 and 2 to Computer 3. + +– Finally, computers 1, 2, and 3 are all *parts_of* network I, which is *instance_of* Object Aggregate. + +**[6]** Using Protege, place these in the BFO hierarchy where you think they fit best: +``` + (a) Bach's Well-Tempered Clavier + (b) Chair of the UB Philosophy Department + (c) SARS-CoV-2 + (d) Mexico City + (e) The trunk of a minivan + (f) Occupation + (g) Ocean + (h) Lake +``` + +**Answer:** + +(a) Bach's Well-Tempered Clavier is_a Generically Dependent Continunat. + +(b) Chair of the UB Philosophy Department is_a Role. + +(c) SARS-CoV-2, as a disease, is_a Disposition. + +(d) Mexico City is_a Site. + +(e) The trunk of a minivan is_a Fiat Object Part. + +(f) Occupation is_a Role. + +(g) Ocean is_a Site. + +(h) Lake is_a Site. + +**[7]** True or False; explain your answers: +``` + (a) An instance of Material Entity can have an instance of Immaterial Entity as part. + (b) An instance of Immaterial Entity can have an instance of Material Entity as part. + (c) An organization may have another organization as part. + (d) An organization may have no members as part. + (e) Any site is partially bounded by some instance of Material Entity. + (f) A book placed under the leg of a wobbly table has acquired a new function. + (g) A glass vase cushioned with packing tape for all time, has the disposition to break. + (h) Spacetime is a class in BFO. + (i) The continuant fiat boundary class of BFO is closed, meaning, there are no subclasses beyond those identified presently in BFO. +``` + +**Answer:** + +(a) True. Boundary or sites are in some cases **continuant parts** of their material hosts (Arp, Smith & Spear 2015: 108). For example, a digestive tube can have its *bona fide* boundary (biological membrane) as part. + +(b) False. According to its definition in BFO, any immaterial entity contains no material entities as parts (Arp, Smith & Spear 2015: 107). + +(c) True. An organization like a company may have a fiat organization part like a labor union, which is itself an organization. + +(d) True. An entity can be an organization if it has members that play specific types of roles *at some time*. So the identity of an organization would not be undermined if it has no members only at some but not all times. + +(e) False. A site, according to its definition in BFO, may be a three-dimensional immaterial part of an immaterial entity (partially or wholly) bounded by a material entity. In this case, the site in question may be itself not partially bounded by a material entity. + +(f) False. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses **because it came into being**. So nothing can acquire a new function after its becoming. + +(g) True. A disposition is usually characterized in terms of stimulus condition and manifestation. The protection provided by packing tape may prevent a glass vase from getting involved in the required stimulus condition and thus manifesting a break, but this does not mean that its disposition to break is thus lost, either. + +(h) False. Strictly speaking, Spatiotemporal Region is a class in BFO, and Spacetime is nothing but the whole of all spatiotemporal regions. + +(i) False. As its entry in BFO file says, Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. + + +**[8]** Model the following scenario in BFO, introducing whatever terms are needed to do so: John runs for 3 hours, starting slowly, speeding up during the middle, then ending the run at a slower pace. + +**Answer:** + +```mermaid +graph LR +A(John) -->|instance_of|B(Object) +C(Running) -->|is_a|D(Process) +E(John's Running) -->|instance_of|C(Running) +A(John) -->|participates_in|E(John's Running) +E(John's Running) -->|starts_with|F(John's Beginning Stage) +E(John's Running) -->|starts_with|G(John's Final Stage) +E(John's Running) -->|has_part|H(John's Middle Stage) +F(John's Beginning Stage)-->|precedes|H(John's Middle Stage) +H(John's Middle Stage)-->|precedes|G(John's Final Stage) +F(John's Beginning Stage) -->|is_a|D(Process) +H(John's Middle Stage) -->|is_a|D(Process) +G(John's Final Stage) -->|is_a|D(Process) +E(John's Running) -->|occurs_in|I(this 3 hours) +I(this 3 hours)-->|instance_of|J(1-D Temporal region) +I(this 3 hours) -->|has_part|P(t1) +I(this 3 hours) -->|has_part|Q(t2) +I(this 3 hours) -->|has_part|R(t3) +P(t1) -->|instance_of|J(1-D Temporal region) +Q(t2) -->|instance_of|J(1-D Temporal region) +R(t3) -->|instance_of|J(1-D Temporal region) +P(t1) -->|precedes|Q(t2) +Q(t2) -->|precedes|R(t3) +F(John's Beginning Stage) -->|occurs_in|P(t1) +H(John's Middle Stage) -->|occurs_in|Q(t2) +G(John's Final Stage) -->|occurs_in|R(t3) +K(Speed) --> |is_a|L(Quality) +B(Object) -->|has_characteristic|L(Quality) +M(John's average speed 1) -->|instance_of|K(Speed) +N(John's average speed 2) -->|instance_of|K(Speed) +O(John's average speed 3) -->|instance_of|K(Speed) +A(John) -->|has_characteristic_at_t1|M(John's average speed 1) +A(John) -->|has_characteristic_at_t2|N(John's average speed 2) +A(John) -->|has_characteristic_at_t3|O(John's average speed 3) +M(John's average speed 1) -->|decreased_in_magnitude_relative_to|N(John's average speed 2) +N(John's average speed 2) -->|increased_in_magnitude_relative_to|O(John's average speed 3) +H(John's Middle Stage) -->|has_part|S(John's accelerating) +G(John's Final Stage) -->|has_part|T(John's decelerating) +S(John's accelerating) -->|is_a|D(Process) +T(John's decelerating) -->|is_a|D(Process) +``` + + This is a graph based on Mermaid, representing the following relations: + +– John (as an Object) *participates_in* John’s running (as a process), and John *has_characteristic_at_t1* John’s average speed 1, and John *has_characteristic_at_t2* John’s average speed 2, and John *has_characteristic_at_t3* John’s average speed 3. All of these speeds are instances of *Quality*. + +– 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. + +– John’s running occurs_in *this 3-hour*, which is instance_of one-dimensional temporal region. This 3-hour also includes 3 *temporal parts*: t1, t2, and t3, each of which is also instance_of one-dimensional temporal region. Besides, t1 *precedes* t2, and t2 *precedes* t3. Moreover, John’s beginning stage occurs_in t1, John’s middle stage occurs_in t2, and John’s final stage occurs_in t3. + +– Change in John’s speed: John's average speed 1 is *decreased_in_magnitude_relative_to* John's average speed 2 (that is, speed 1＜speed 2), and John's average speed 2 is *increased_in_magnitude_relative_to* John's average speed 3 (that is, speed 2＞speed 3). Moreover, John's Middle Stage has_part John's accelerating, and John's Final Stage has_part John's decelerating. + +**[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. + +**Answer:** + +Pellet, as a reasoning tool, supports incremental reasoning in the sense that it can only do reasoning over new changes made to an ontology, rather than re-calculating the entire ontology from scratch. It can do this because it can identify an ontology's parts which are affected by new changes, and quickly retrieve previously stored results to assist its new reasoning. + +Imagine we are playing a game: You continuously tell me what is a thing like without giving its name until I correctly guess what it is. Suppose you are describing a dog. You say, "It has a tail, four legs, two pointy ears and so on." I guess that it is a dog and that is right. Now you further require me to guess what particular kind of dog it is. So you continue to say, "Oh, it is as high as a wood table, as long as a small trolley, and has beautiful golden fur!" I don't have to re-reason over all information you give. Rather, I still remember that I infer by previous information that it is a dog, so I can only make a guess on the basis of new information, especially the fact that it has golden fur. Therefore, I guess it is a golden retriever and I get it right. This is an example of incremental reasoning, and Pellet performs such reasonings just as I infer that the thing is a golden retriever. + +So if you have a very large set of data or ontology, and the data set or ontology is in frequent change, then you wanna use Pellet for incremental reasoning. It can save a lot of time, promote cooperation among different users, and free them from heavy but boring tasks of calculation. + +**[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). + +**Answer:** + +| *Pairwise* | Functional | InverseFun | Transitive | Symmetric | Asymmetric | Reflexive | Irreflexive | +| --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | +| **Functional** | (*N/A*) | YES | NO | YES | YES | YES | YES | +| **InverseFun** | YES | (*N/A*) | NO | YES | YES | YES | YES | +| **Transitive** | NO | NO | (*N/A*) | YES | NO | YES | NO | +| **Symmetric** | YES | YES | YES | (*N/A*) | NO | YES | YES | +| **Asymmetric** | YES | YES | NO | NO | (*N/A*) | NO | YES | +| **Reflexive** | YES | YES | YES | YES | NO | (*N/A*) | NO | +| **Irreflexive** | YES | YES | NO | YES | YES | NO | (*N/A*) | + + +**Note**: In the above table, there are 21 different sorts of possibilities in total. We use "Yes" to represent a case where a pair of object property characteristics can be combined, and "No" to represent a case where a pair of object property characteristics cannot be combined. + +As a result, we find that there are 7 sorts of cases where a pair of object property characteristics cannot be combined: + +(1) The following 3 pairs cannot be combined because of a logical contradiction: + +*Asymmetric & Reflexive, Asymmetric & Symmetric, and Reflexive & Irreflexive.* + +(2) The following 4 pairs cannot be combined because of a more subtle factor. That is, an assertion of transitivity leads to a result that the target object property becomes **non-simple** (see Baader's book: section 8.1, page 211), so it is beyond the capacity limit of the reasoner: + +*Transitive & Functional, Transitive & Inverse Functional, Transitive & Asymmetric, and Transitive & Irreflexive.* diff --git a/Project-3/Proj_3RO.owl b/Project-3/Proj_3RO.owl new file mode 100644 index 00000000..d509ab7e --- /dev/null +++ b/Project-3/Proj_3RO.owl @@ -0,0 +1,14080 @@ + + + + BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. + BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. + BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. + Alan Ruttenberg + Albert Goldfain + Barry Smith + Bill Duncan + Bjoern Peters + Chris Mungall + David Osumi-Sutherland + Fabian Neuhaus + Holger Stenzhorn + James A. Overton + Janna Hastings + Jie Zheng + Jonathan Bona + Larry Hunter + Leonard Jacuzzo + Ludger Jansen + Mark Ressler + Mathias Brochhausen + Mauricio Almeida + Melanie Courtot + Pierre Grenon + Randall Dipert + Ron Rudnicki + Selja Seppälä + Stefan Schulz + Thomas Bittner + Werner Ceusters + Yongqun "Oliver" He + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. + OBO Relations Ontology + + + Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. + The BSD license on the BFO project site refers to code used to build BFO. + This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. + + + + + + + + 2023-02-22 + + + + https://github.com/oborel/obo-relations/ + + + + + + + + + + + + + + + + + + + + Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. + Really of interest to developers only + BFO OWL specification label + + + + + + + + + Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 + Person:Alan Ruttenberg + Really of interest to developers only + BFO CLIF specification label + + + + + + + + + + editor preferred term + + + + + + + + + example of usage + + + + + + + + + + + + + + + definition + definition + + + + + + + + + editor note + + + + + + + + + term editor + + + + + + + + + alternative term + + + + + + + + + definition source + + + + + + + + + curator note + + + + + + + + + imported from + + + + + + + + + + + + + + + + + + + + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + + + + + + + + + + OBO foundry unique label + + + + + + + + + elucidation + + + + + + + + + has associated axiom(nl) + + + + + + + + + has associated axiom(fol) + + + + + + + + + + + + + + + has axiom label + + + + + + + + + term replaced by + + + + + + + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + defined by construct + + + + + + + + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + temporal interpretation + + + + + + + + + + tooth SubClassOf 'never in taxon' value 'Aves' + x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. + + + + Class: ?X DisjointWith: RO_0002162 some ?Y + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> +PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?x owl:disjointWith [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . + ?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom [ + a owl:Class ; + owl:complementOf ?taxon + ] + ] . +} +WHERE { + ?x never_in_taxon: ?taxon . +} + never in taxon + + + + + + + + + + A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. + non-overlapping with + shares no parts with + + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) + PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> +PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> +CONSTRUCT { + part_of: a owl:ObjectProperty . + [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?x ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?y + ] + ] +} +WHERE { + ?x mutually_spatially_disjoint_with: ?y . +} + mutually spatially disjoint with + + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + + + + + + + + + An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + taxonomic class assertion + + + + + + + + + + S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] + ambiguous for taxon + + + + + + + + + + S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. + + + This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost + dubious for taxon + + + + + + + + + + S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S + + + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> +PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?witness rdfs:label ?label . + ?witness rdfs:subClassOf ?x . + ?witness rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . +} +WHERE { + ?x present_in_taxon: ?taxon . + BIND(IRI(CONCAT( + "http://purl.obolibrary.org/obo/RO_0002175#", + MD5(STR(?x)), + "-", + MD5(STR(?taxon)) + )) as ?witness) + BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) +} + The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. + present in taxon + + + + + + + + + + defined by inverse + + + + + + + + + An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + logical macro assertion + http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ + + + + + + + + An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + annotation property cardinality + + + + + + + + + + A logical macro assertion whose domain is an IRI for a class + The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL + logical macro assertion on a class + + + + + + + + + A logical macro assertion whose domain is an IRI for a property + logical macro assertion on a property + + + + + + + + + Used to annotate object properties to describe a logical meta-property or characteristic of the object property. + logical macro assertion on an object property + + + + + + + + + logical macro assertion on an annotation property + + + + + + + + + An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + dispositional interpretation + + + + + + + + + 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' + A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. + shares no connection with + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) + has no connections with + + + + + + + + + inherited annotation property + + + + + + + + Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + curator guidance link + + + + + + + + + brain always_present_in_taxon 'Vertebrata' + forelimb always_present_in_taxon Euarchontoglires + S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S + This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. + never lost in + always present in taxon + + + + + + + + + This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. + temporal logical macro assertion on a class + + + + + + + + + measurement property has unit + + + + + + + + + has start time value + + + + + + + + + + has end time value + + + + + + + + + + Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + start, days post fertilization + + + + + + + + + + Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + end, days post fertilization + + + + + + + + + + Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + start, years post birth + + + + + + + + + + Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + end, years post birth + + + + + + + + + + Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + start, months post birth + + + + + + + + + + Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + end, months post birth + + + + + + + + + + Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + month of gestation + + + + + + + + + + A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + has developmental stage marker + + + + + + + + + + Count of number of days intervening between the start of the stage and the time of coitum. + For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + start, days post coitum + + + + + + + + + + Count of number of days intervening between the end of the stage and the time of coitum. + end, days post coitum + + + + + + + + + + start, weeks post birth + + + + + + + + + + end, weeks post birth + + + + + + + + + + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + is asymmetric relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + is symmetric relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + is relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y + The general property hierarchy is: + + "directly P" SubPropertyOf "P" + Transitive(P) + +Where we have an annotation assertion + + "directly P" "is direct form of" "P" + If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' + + is direct form of + + + + + + + + + + relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y + + is indirect form of + + + + + + + + + + logical macro assertion on an axiom + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + is relational form of a class + + + + + + + + + A shortcut relationship that holds between two entities based on their identity criteria + logical macro assertion involving identity + + + + + + + + + A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + in approximate one to one relationship with + + + + + + + + + x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y + The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + is approximately equivalent to + + + + + + + + + 'anterior end of organism' is-opposite-of 'posterior end of organism' + 'increase in temperature' is-opposite-of 'decrease in temperature' + x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is opposite of + + + + + + + + + x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is indistinguishable from + + + + + + + + + evidential logical macro assertion on an axiom + + + + + + + + + A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom has evidence + + + + + + + + + A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom contradicted by evidence + + + + + + + + + In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. + this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. + If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion + is representative IRI for equivalence set + OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member + + + + + + + + + true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. + + nominally disjoint with + + + + + + + + + Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" + + 2018-03-13T23:59:29Z + is directional form of + + + + + + + + + + 2018-03-14T00:03:16Z + is positive form of + + + + + + + + + + 2018-03-14T00:03:24Z + is negative form of + + + + + + + + + part-of is homeomorphic for independent continuants. + R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. + + 2018-10-21T19:46:34Z + R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. + is homeomorphic for + + + + + + + + + + pg + 2020-09-22T11:05:29Z + valid_for_go_annotation_extension + + + + + + + + + + pg + 2020-09-22T11:05:18Z + valid_for_go_gp2term + + + + + + + + + + pg + 2020-09-22T11:04:12Z + valid_for_go_ontology + + + + + + + + + + pg + 2020-09-22T11:05:45Z + valid_for_gocam + + + + + + + + + + eco subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subset_property + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_broad_synonym + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_format_version + + + + + + + + has_related_synonym + + + + + + + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + is defined by + + + + + is defined by + This is an experimental annotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + part of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + + + + has part + + + + + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + accidentally included in BFO 1.2 proposal + - should have been BFO_0000062 + obsolete preceded by + true + + + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. + derives from part of + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + has characteristic + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete upstream in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete downstream in neural circuit with + true + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + is location of + my head is the location of my brain + this cage is the location of this rat + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + location_of + + location of + + + + + + + + + + + + + contained in + Containment is location not involving parthood, and arises only where some immaterial continuant is involved. + Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): + Intended meaning: +domain: material entity +range: spatial region or site (immaterial continuant) + + contained_in + + + contained in + + + + + + + + contains + + + contains + + + + + + + + + + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is allergic trigger for + + + + + + + + + + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is autoimmune trigger for + + + + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has allergic trigger + + + + + + + + + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has autoimmune trigger + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + + located in + + + + + + + + + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of + surface of + + 2D boundary of + + + + + + + + + + May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 + + + aligned with + + + + + + + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + + has boundary + has_2D_boundary + + has 2D boundary + + + + + + + + + A relation that holds between two neurons that are electrically coupled via gap junctions. + + + electrically_synapsed_to + + + + + + + + + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + + tracheates + + + + + + + + + + http://www.ncbi.nlm.nih.gov/pubmed/22402613 + innervated_by + + + + + + + + + + + + has synaptic terminal of + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + bounding layer of + + + + + + + + + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + Note from NCEAS meeting: consider changing primary label + + + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + coincident with + + + + + + + + + A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. + + x 'cell expresses' y iff: +cell(x) +AND gene(y) +AND exists some 'transcription, DNA templated (GO_0006351)'(t) +AND t occurs_in x +AND t has_input y + cell expresses + + + + + + + + + x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + regulates in other organism + + + + + + + + + + + + A relationship that holds between a process that regulates a transport process and the entity transported by that process. + + + regulates transport of + + + + + + + + + + A part of relation that applies only between occurrents. + occurrent part of + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. + dos + 2017-07-20T17:11:08Z + transports + + + + + + + + + A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. + dos + 2017-07-20T17:19:37Z + occurs across + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + A relationship that holds between two images, A and B, where: +A depicts X; +B depicts Y; +X and Y are both of type T' +C is a 2 layer image consiting of layers A and B; +A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. +Note: A and B may be 2D or 3D. +Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. + dos + 2017-12-07T12:58:06Z + in register with + + + + + A relationship that holds between two images, A and B, where: +A depicts X; +B depicts Y; +X and Y are both of type T' +C is a 2 layer image consiting of layers A and B; +A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. +Note: A and B may be 2D or 3D. +Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. + GOC:dos + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + + + + + David Osumi-Sutherland + + starts before + + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + + + + + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + + + + + Relation between a neuron and an anatomical structure that its soma is part of. + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) + + has soma location + + + + + + + + + + + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + + fasciculates with + (forall (?x ?y) + (iff + (fasciculates_with ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron ; CL_0000540" ?x) + ("neuron projection bundle ; CARO_0001001" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500' " ?npbs) + (part_of ?npbs ?y) + (part_of ?nps ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + fasciculates with + + + + + + + + + + + + + + Relation between a neuron and some structure its axon forms (chemical) synapses in. + + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( + <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) + + + axon synapses in + + + + + + + + + + + Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + synapsed by + + + + + + + + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] + + Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. + + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) + + has plasma membrane part + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. + + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_Ib_bouton_to + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. + + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_Is_bouton_to + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type II bouton. + + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_II_bouton_to + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type II bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_II_bouton + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_Ib_bouton + + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + + + synapsed in + http://purl.obolibrary.org/obo/BFO_0000051 some ( + http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( + http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) + + + has postsynaptic terminal in + + + + + + + + + has neurotransmitter + releases neurotransmitter + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_Is_bouton + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + synapses in + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) + + + has presynaptic terminal in + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type III bouton. + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_III_bouton_to + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type III bouton. + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_III_bouton + + + + + + + + + + Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + N1 synapsed_to some N2 +Expands to: +N1 SubclassOf ( + has_part some ( + ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( + ‘synapse ; GO:0045202’ that has_part some ( + ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) + synapsed to + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. + + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( + http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( + <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) + + + dendrite synapsed in + + + + + + + + + + + + + + A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. + + has synapse in + <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) + + + has synaptic terminal in + + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + + overlaps + + + + + + + + + true + + + + + + + + + + The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + + has fasciculating component + (forall (?x ?y) + (iff + (has_fasciculating_neuron_projection ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron projection bundle ; CARO_0001001" ?x) + ("neuron projection ; GO0043005" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500" ?npbs) + (part_of ?nps ?y) + (part_of ?npbs ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + + + + has fasciculating neuron projection + + + + + + + + + + + + + Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + innervates + + + + + + + + + + + X continuous_with Y if and only if X and Y share a fiat boundary. + + connected to + The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + + continuous with + FMA:85972 + + + + + + + + + + x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom + proper overlaps + (forall (?x ?y) + (iff + (proper_overlaps ?x ?y) + (and + (overlaps ?x ?y) + (not (part_of ?x ?y)) + (not (part_of ?y ?x))))) + + + partially overlaps + + + + + + + + + + + + d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + ancestral_stucture_of + evolutionarily_descended_from + derived by descent from + + + + + + + + + + + inverse of derived by descent from + + has derived by descendant + + + + + + + + + + + + + + + + two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + Consider obsoleting and merging with child relation, 'in homology relationship with' + VBO calls this homologous_to + shares ancestor with + + + + + + + + + + + + serially homologous to + + + + + + + + + lactation SubClassOf 'only in taxon' some 'Mammalia' + + x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria + + + + only in taxon + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + + + + + + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + A is spatially_disjoint_from B if and only if they have no parts in common + There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. + + + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy + BFO_0000051 exactly 0 (BFO_0000050 some ?Y) + + + spatially disjoint from + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + + + + + + + + + + + + + + + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + + connected to + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + + + + + + + + + The M8 connects Glasgow and Edinburgh + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + + connects + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + + + + + + + + + + + + + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) + attached to part of + + + + + + + + + true + + + + + + + + + Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + + supplies + + + + + + + + + Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure + + drains + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + + + has phenotype + + + + + + + + + + inverse of has phenotype + + + + phenotype of + + + + + + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + + + + + This is the transitive form of the develops from relation + develops from + + + + + + + + + + + + + inverse of develops from + + + + + develops into + + + + + + + + + + + + + + + definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" + We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. + + gene product of + + + + + + + + + + + + + every HOTAIR lncRNA is the gene product of some HOXC gene + every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene + + x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y + + has gene product + + + + + + + + + + + + + + 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' + + x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process + + expressed in + + + + + + + + + + + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. + + + FBbt + + has developmental precursor + TODO - add child relations from DOS + directly develops from + + + + + + + + + + A parasite that kills or sterilizes its host + parasitoid of + + + + + + + + + inverse of parasitoid of + + has parasitoid + + + + + + + + + + inverse of directly develops from + developmental precursor of + + directly develops into + + + + + + + + + + + + + + + + + + + + + + + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. + + + + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + + + regulates + + + + + + + + + + + + + + + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. + + + negatively regulates (process to process) + + + + + negatively regulates + + + + + + + + + + + + + + + + + + + + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. + + + positively regulates (process to process) + + + + + positively regulates + + + + + + + + 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) + heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') + + x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + TODO: add homeomorphy axiom + This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. + + has prototype + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + + capable of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + + has function in + capable of part of + + + + + + + + + + true + + + + + + + + OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role + + agent in + + Obsoleted as the inverse property was obsoleted. + obsolete actively participates in + true + + + + + + + + OBSOLETE x has participant y if and only if x realizes some active role that inheres in y + + has agent + + obsolete has active participant + true + + + + + + + + + + + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + + + surrounded by + + + + + + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + The epidermis layer of a vertebrate is adjacent to the dermis. + The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. + The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. + + x adjacent to y if and only if x and y share a boundary. + This relation acts as a join point with BSPO + + + + + + adjacent to + + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + + + + + + + + + + + inverse of surrounded by + + + + surrounds + + + + + + + + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + inverse of starts with + + Chris Mungall + Allen + + starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + started by + + starts with + + + + + + + + + + + + + + x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + + develops from part of + + + + + + + + + + + + + + x develops_in y if x is located in y whilst x is developing + + EHDAA2 + Jonathan Bard, EHDAA2 + develops in + + + + + + + + + A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. + obligate parasite of + + + + + + + + + A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. + facultative parasite of + + + + + + + + + + + + inverse of ends with + + Chris Mungall + + ends + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + finished by + + ends with + + + + + + + + + + + + + + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + + starts with process that occurs in + + has start location + + + + + + + + + + + + + + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + + ends with process that occurs in + + has end location + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + + + + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + + produces + + + + + has output + + + + + + + + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) + stem parasite of + + + + + + + + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) + root parasite of + + + + + + + + + A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. + hemiparasite of + + + + + + + + + X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. + + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). + +If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant + + + + + + + + + A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. + ExO:0000001 + has exposure receptor + + + + + + + + + A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. + ExO:0000000 + has exposure stressor + + + + + + + + + A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor + ExO:0000055 + has exposure route + + + + + + + + + A broad relationship between an exposure event or process and the course takes from the source to the target. + http://purl.obolibrary.org/obo/ExO_0000004 + has exposure transport path + + + + + + + + + Any relationship between an exposure event or process and any other entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. + related via exposure to + + + + + + + + + g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. + over-expressed in + + + + + + + + + g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. + under-expressed in + + + + + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. + has active substance + has active pharmaceutical ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + + active ingredient in + + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. + b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. + + connecting branch of + + + + + + + + + + inverse of connecting branch of + + + has connecting branch + + + + + + + + + + + + + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + + x has developmental contribution from y iff x has some part z such that z develops from y + + has developmental contribution from + + + + + + + + + + + + + + + inverse of has developmental contribution from + + + developmentally contributes to + + + + + + + + + + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T + + + + induced by + + Developmental Biology, Gilbert, 8th edition, figure 6.5(F) + GO:0001759 + We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] + developmentally induced by + + + + + + + + + + + Inverse of developmentally induced by + + developmentally induces + + + + + + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + false + + In general you should not use this relation to make assertions - use one of the more specific relations below this one + This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + developmentally preceded by + + + + + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + + acts upstream of or within + + + + + + + + + + + x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else + This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage + + replaces + developmentally replaces + + + + + + + + + + Inverse of developmentally preceded by + + developmentally succeeded by + + + + + + + + + + + + + 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue + + + part of developmental precursor of + + + + + + + + + + + x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x + Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. + + ubiquitously expressed in + + + + + + + + + + Inverse of 'expressed in' + + expresses + + + + + + + + + + inverse of ubiquiotously expressed in + + + ubiquitously expresses + + + + + + + + + + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + + results in developmental progression of + + + + + + + + + + + every flower development (GO:0009908) results in development of some flower (PO:0009046) + + p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + + http://www.geneontology.org/GO.doc.development.shtml + + + + results in development of + + + + + + + + + + + an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + + GOC:mtg_berkeley_2013 + + + + results in formation of + + + + + + + + + + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. + tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) + + The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + + GOC:mtg_berkeley_2013 + + + + results in morphogenesis of + + + + + + + + + + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process + bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) + + The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + + GOC:mtg_berkeley_2013 + + + + results in maturation of + + + + + + + + + foramen ovale closure SubClassOf results in disappearance of foramen ovale + + + May be merged into parent relation + results in disappearance of + + + + + + + + + every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) + + + May be merged into parent relation + results in developmental regression of + + + + + + + + + + Inverse of 'is substance that treats' + + + is treated by substance + + + + + + + + + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' +where +'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview + + x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. + + adapted for living in + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. + has habitat + + + + + + + + + + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. + + + + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. + + + + + causally upstream of, negative effect + + + + + + + + + A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. + + + + + 2017-06-05T17:35:04Z + has exposure stimulus + + + + + + + + + + evolutionary variant of + + + + + + + + + + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. + + regulates localization of + + + + transports or maintains localization of + + + + + + + + + + + + + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + + + + + + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + + GOC:mtg_berkeley_2013 + + + + results in acquisition of features of + + + + + + + + A relationship that holds via some environmental process + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + evolutionarily related to + + + + + + + + A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + ecologically related to + + + + + + + + + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. + + adapted for + + confers advantage in + + + + + + + + A mereological relationship or a topological relationship + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + developmentally related to + + + + + + + + + Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) + a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. + + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] + + colocalizes with + + + + + + + + + + ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. + Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. + eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex + We would like to say + +if and only if + exists c', p' + c part_of c' and c' capable_of p + and + c capable_of p' and p' part_of p +then + c contributes_to p + +However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. + + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + + contributes to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. + + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + + This is a grouping relation that collects relations used for the purpose of connecting structure and function + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + + false + part of structure that is capable of + + + + + + + + + true + + + + + + + + holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism + genomically related to + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + + actively involved in + enables part of + involved in + + + + + + + + + + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid + p regulates levels of c if p regulates some amount (PATO:0000070) of c + + + regulates levels of (process to entity) + regulates levels of + + + + + + + + + + inverse of enables + + + enabled by + + + + + + + + + + inverse of regulates + + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + + + negatively regulated by + + + + + + + + + inverse of positively regulates + + + positively regulated by + + + + + + + + A relationship that holds via some process of localization + + Do not use this relation directly. It is a grouping relation. + related via localization to + + + + + + + + + + + + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. + + + + + has target start location + + + + + + + + + + + + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. + + + + + has target end location + + + + + + + + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. + + + imports + + + + + + + + + Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l + + results in transport along + + + + + + + + + + Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. + + + results in transport across + + + + + + + + + + 'pollen tube growth' results_in growth_of some 'pollen tube' + + results in growth of + + + + + + + + + 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) + + results in transport to from or in + + + + + + + + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + + + exports + + + + + + + + + an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. + p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. + + + + + results in commitment to + + + + + + + + + p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. + + + + + results in determination of + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + + + + input of + + + + + + + + + + inverse of has output + + + + output of + + + + + + + + + + formed as result of + + + + + + + + + + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. + + results in structural organization of + + + + + + + + + The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. + + + + + results in specification of + + + + + + + + + p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. + + results in developmental induction of + + + + + + + + + + http://neurolex.org/wiki/Property:DendriteLocation + has dendrite location + + + + + + + + + + + a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a + + attached to (anatomical structure to anatomical structure) + + attached to + + + + + + + + + + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + + Wikipedia:Insertion_(anatomy) + has muscle origin + + + + + + + + + + + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + + Wikipedia:Insertion_(anatomy) + has muscle insertion + + + + + + + + + + false + + x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + + + has fused element + A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + derived from ancestral fusion of + + + + + + + + + + A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + + in branching relationship with + + https://github.com/obophenotype/uberon/issues/170 + + + + + + + + + + Deschutes River tributary_of Columbia River + inferior epigastric vein tributary_of external iliac vein + + x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. + + drains into + drains to + tributary channel of + http://en.wikipedia.org/wiki/Tributary + http://www.medindia.net/glossary/venous_tributary.htm + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) + + tributary of + + http://en.wikipedia.org/wiki/Tributary + + + + + + + + + + Deschutes River distributary_of Little Lava Lake + + x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x + + branch of + distributary channel of + http://en.wikipedia.org/wiki/Distributary + + This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes + distributary of + + + + + + + + + + + + + + + + + x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + + anastomoses with + + anabranch of + + + + + + + + + + + + + + + A lump of clay and a statue + x spatially_coextensive_with y if and inly if x and y have the same location + + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + spatially coextensive with + + + + + + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S + x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y + + + branching part of + + FMA:85994 + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. + + x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. + + + main stem of + + + + + + + + + + + x proper_distributary_of y iff x distributary_of y and x does not flow back into y + + + proper distributary of + + + + + + + + + + x proper_tributary_of y iff x tributary_of y and x does not originate from y + + + proper tributary of + + + + + + + + + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + + has developmental potential involving + + + + + + + + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + + has potential to developmentally contribute to + + + + + + + + + + x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + + has potential to developmentally induce + + + + + + + + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + + has potential to develop into + + + + + + + + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + + has potential to directly develop into + + + + + + + + + + + + + 'protein catabolic process' SubClassOf has_direct_input some protein + + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + directly consumes + This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' + has direct input + + + + + + + + + + Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + obsolete has indirect input + true + + + + + + + + translation SubClassOf has_direct_output some protein + + p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + + directly produces + obsolete has direct output + true + + + + + + + + + + + + + + Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + obsolete has indirect output + true + + + + + + + + + + + + inverse of upstream of + + causally downstream of + + + + + + + + + + + + + immediately causally downstream of + + + + + + + + + This term was obsoleted because it has the same meaning as 'directly positively regulates'. + obsolete directly activates + true + + + + + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + + indirectly activates + + indirectly positively regulates + + + + + + + + + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + obsolete directly inhibits + true + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + + indirectly inhibits + + indirectly negatively regulates + + + + + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + + + + + + + + + + + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. + + + + causally upstream of + + + + + + + + + + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. + + + immediately causally upstream of + + + + + + + + + + + + + + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. + This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit + + directly provides input for + + directly provides input for (process to process) + provides input for + + + + + + + + + + + transitive form of directly_provides_input_for + + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. + transitively provides input for (process to process) + transitively provides input for + + + + + + + + + + + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + + influences (processual) + affects + causally upstream of or within + + + + + + + + false + + This is an exploratory relation + differs in + https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions + + + + + + + + + + differs in attribute of + + + + + + + + + + differs in attribute + + + + + + + + + + inverse of causally upstream of or within + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. + + contributes to morphology of + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Considering relabeling as 'pairwise interacts with' + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 + + + + + + + + + + An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) + + genetically interacts with + + http://purl.obolibrary.org/obo/MI_0208 + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + + + An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. + + interacts with on organism level + + biotically interacts with + + http://eol.org/schema/terms/interactsWith + + + + + + + + + An interaction relationship in which the partners are related via a feeding relationship. + + + trophically interacts with + + + + + + + + + + + A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] + Baleen whale preys on krill + An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members + + + + is subject of predation interaction with + preys upon + + preys on + http://eol.org/schema/terms/preysUpon + http://www.inaturalist.org/observations/2942824 + + + + + + + + + + + + + + + + + A biotic interaction in which the two organisms live together in more or less intimate association. + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + + symbiotically interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + commensually interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + mutualistically interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + This relation groups a pair of inverse relations, parasite of and parasitized by + + interacts with via parasite-host interaction + + + + + + + + + + + + + + + + + + Pediculus humanus capitis parasite of human + + parasitizes + direct parasite of + + parasite of + http://eol.org/schema/terms/parasitizes + + + + + + + + + + + has parasite + parasitised by + directly parasitized by + + parasitized by + http://eol.org/schema/terms/hasParasite + + + + + + + + + Porifiera attaches to substrate + A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. + + semibiotically interacts with + + participates in a abiotic-biotic interaction with + + + + + + + + + + + + + + + Axiomatization to GO to be added later + + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + + + molecularly controls + directly regulates activity of + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + + + directly inhibits + molecularly decreases activity of + directly negatively regulates activity of + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + + + directly activates + molecularly increases activity of + directly positively regulates activity of + + + + + + + + + all dengue disease transmitted by some mosquito + A relationship that holds between a disease and organism + Add domain and range constraints + + transmitted by + + + + + + + + + A relation that holds between a disease or an organism and a phenotype + + has symptom + + + + + + + + + + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + + host of + + + + + + + + + X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y + + + has host + http://eol.org/schema/terms/hasHost + + + + + + + + + + Bees pollinate Flowers + This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. + + is subject of pollination interaction with + + pollinates + http://eol.org/schema/terms/pollinates + + + + + + + + + + has polinator + is target of pollination interaction with + + pollinated by + http://eol.org/schema/terms/hasPollinator + + + + + + + + + + + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. + + acquires nutrients from + + + + + + + + + inverse of preys on + + has predator + is target of predation interaction with + + + preyed upon by + http://eol.org/schema/terms/HasPredator + http://polytraits.lifewatchgreece.eu/terms/PRED + + + + + + + + + + Anopheles is a vector for Plasmodium + + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism + + is vector for + + + + + + + + + + + has vector + + + + + + + + + + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + partner in + + + + + + + + + + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + subject participant in + + + + + + + + + + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + target participant in + + + + + + + + + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + + + + + + + + + + is symbiosis + + + + + + + + + + is commensalism + + + + + + + + + + is mutualism + + + + + + + + + + is parasitism + + + + + + + + + + + provides nutrients for + + + + + + + + + + is subject of eating interaction with + + eats + + + + + + + + + + eaten by + is target of eating interaction with + + is eaten by + + + + + + + + + + A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and +the a supports either the existence of b, or the truth value of b. + + + is evidence for + + + + + + + + + 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' + x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. + + + + + composed primarily of + + + + + + + + + ABal nucleus child nucleus of ABa nucleus (in C elegans) + c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. + child nucleus of + + + + + + + + + A child nucleus relationship in which the cells are part of a hermaphroditic organism + + child nucleus of in hermaphrodite + + + + + + + + + A child nucleus relationship in which the cells are part of a male organism + + child nucleus of in male + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + + + has part that occurs in + + + + + + + + + true + + + + + + + + + + + + + + An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y + Axiomatization to GO to be added later + + ubiquitinates + + + + + + + + + + is kinase activity + + + + + + + + + + is ubiquitination + + + + + + + + + + See notes for inverse relation + + receives input from + + + + + + + + + This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. + + sends output to + + + + + + + + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + relation between physical entity and a process or stage + + + + + + + + + + + + + + + + + + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + + existence starts during + + + + + + + + + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + + existence starts with + + + + + + + + + x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence overlaps + + + + + + + + + + x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + + exists during + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts and ends during + + + + + + + + + + + + + + + + + + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during + + + + + + + + + x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends with + + + + + + + + + + x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships + + transformation of + + + + + + + + + + x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t + + + immediate transformation of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts during or after + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during or before + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + towards + + + + + + + + + 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate + p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c + + has intermediate product + + has intermediate + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between entities + + + + + + + + + + + + A coral reef environment is determined by a particular coral reef + s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. + The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + + + determined by (system to material entity) + + + + determined by + + + + + + + + + inverse of determined by + + determines (material entity to system) + + + determines + + + + + + + + + + + + + + s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. + + + determined by part of + + + + + + + + + true + + + + + + + + + + x is transcribed from y if and only if x is synthesized from template y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed from + + + + + + + + + inverse of transcribed from + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + transcribed to + + + + + + + + + + x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + ribosomal translation of + + + + + + + + + inverse of ribosomal translation of + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + ribosomally translates to + + + + + + + + A relation that holds between two entities that have the property of being sequences or having sequences. + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + + sequentially related to + + + + + + + + + Every UTR is adjacent to a CDS of the same transcript + Two consecutive DNA residues are sequentially adjacent + Two exons on a processed transcript that were previously connected by an intron are adjacent + x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + sequentially adjacent to + + + + + + + + + + + Every CDS has as a start sequence the start codon for that transcript + x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + + started by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has start sequence + + + + + + + + + + inverse of has start sequence + + starts + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + is start sequence of + + + + + + + + + + + Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) + x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + + ended by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has end sequence + + + + + + + + + + inverse of has end sequence + + ends + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + is end sequence of + + + + + + + + + x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. + In the SO paper, this was defined as an instance-type relation + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + is consecutive sequence of + + + + + + + + + + Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. + x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering + + + is sequentially aligned with + + + + + + + + + + + The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + + + bounds sequence of + + + + + + + + + + inverse of bounds sequence of + + + + is bound by sequence of + + + + + + + + + + + + + x has subsequence y iff all of the sequence parts of y are sequence parts of x + + contains + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has subsequence + + + + + + + + + + + + inverse of has subsequence + + contained by + + + is subsequence of + + + + + + + + + + + + + + + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + + + overlaps sequence of + + + + + + + + + + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + + disconnected from + + does not overlap sequence of + + + + + + + + + + inverse of downstream of sequence of + + + is upstream of sequence of + + + + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + + + is downstream of sequence of + + + + + + + + + + A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript + x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + + + + is immediately downstream of sequence of + + + + + + + + + + A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript + inverse of immediately downstream of + + + is immediately upstream of sequence of + + + + + + + + + + + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' + A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. + + has supporting framework + The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). + has skeleton + + + + + + + + + + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. + + results in ending of + + + + + + + + + + + + + + x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism + + http://eol.org/schema/terms/hyperparasitoidOf + https://en.wikipedia.org/wiki/Hyperparasite + hyperparasitoid of + epiparasite of + + hyperparasite of + + + + + + + + + + + + + inverse of hyperparasite of + + has epiparasite + has hyperparasite + hyperparasitoidized by + + + hyperparasitized by + + + + + + + + + + http://en.wikipedia.org/wiki/Allelopathy + + allelopath of + http://eol.org/schema/terms/allelopathyYes + x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y + + + + + + + + + + + + pathogen of + + + + + + + + + + + has pathogen + + + + + + + + + inverse of is evidence for + + + + + x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. + has evidence + + + + + + + + + + + + causally influenced by (entity-centric) + causally influenced by + + + + + + + + + + interaction relation helper property + + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + + molecular interaction relation helper property + + + + + + + + + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c + + + + + + results in movement of + + + + + + + + + + + + + + + + + + + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + + + + causally influences (entity-centric) + causally influences + + + + + + + + + A relation that holds between elements of a musculoskeletal system or its analogs. + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. + biomechanically related to + + + + + + + + + m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. + + Wikipedia:Antagonist_(muscle) + has muscle antagonist + + + + + + + + + + + inverse of branching part of + + + + has branching part + + + + + + + + + x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. + + UBERON:cjm + This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. + + conduit for + + + + + + + + + x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + + GOC:cjm + + lumen of + + + + + + + + + s is luminal space of x iff s is lumen_of x and s is an immaterial entity + + + luminal space of + + + + + + + + A relation that holds between an attribute or a qualifier and another attribute. + + + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + + has modifier + + + + + + + + + + + participates in a biotic-biotic interaction with + + + + + + + + + + inverse of has skeleton + + + skeleton of + + + + + + + + + + p directly regulates q iff p is immediately causally upstream of q and p regulates q. + + + directly regulates (processual) + + + + + directly regulates + + + + + + + + + holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y). + existence starts at end of + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + + has part structure that is capable of + + + + + + + + + + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. + results in closure of + + + + + + + + + p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + results in breakdown of + + + + + + + + + results in synthesis of + + + + + + + + + + + + + results in assembly of + + + + + + + + + p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + results in catabolism of + + + + + + + + + + results in disassembly of + + + + + + + + + + results in remodeling of + + + + + + + + + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + results in organization of + + + + + + + + + holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y). + existence ends at start of + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + pazopanib -> pathological angiogenesis + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + treats + + The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. + capable of inhibiting or preventing pathological process + + + + + treats + Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + + + + + + + + + benzene -> cancer [CHEBI] + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + causes disease + + capable of upregulating or causing pathological process + + + + + + + + + c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. + treats + + is substance that treats + + + + + + + + + + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. + May be ceded to OBI + is marker for + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + obsolete related via dependence to + true + + + + + + + + A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Groups both positive and negative correlation + correlated with + + + + + + + + + An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. + A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. + In the Gene Ontology association model, this corresponds to the With/From field + is evidence with support from + + + + + + + + + Inverse of is-model-of + has model + + + + + + + + Do not use this relation directly. It is a grouping relation. + related via evidence or inference to + + + + + + + + + + visits + https://github.com/oborel/obo-relations/issues/74 + + + + + + + + + visited by + + + + + + + + + + visits flowers of + + + + + + + + + has flowers visited by + + + + + + + + + + + lays eggs in + + + + + + + + + + has eggs laid in by + + + + + + + + + + https://github.com/jhpoelen/eol-globi-data/issues/143 + kills + + + + + + + + + is killed by + + + + + + + + + + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. + + directly positively regulates (process to process) + + + + + directly positively regulates + + + + + + + + + + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. + + directly negatively regulates (process to process) + + + + + directly negatively regulates + + + + + + + + + + A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host + + ectoparasite of + + + + + + + + + inverse of ectoparasite of + + has ectoparasite + + + + + + + + + + + A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system + lives inside of + endoparasite of + + + + + + + + + has endoparasite + + + + + + + + + + A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite + mesoparasite of + + + + + + + + + inverse of mesoparasite of + + has mesoparasite + + + + + + + + + + A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. + + intercellular endoparasite of + + + + + + + + + inverse of intercellular endoparasite of + + has intercellular endoparasite + + + + + + + + + + A sub-relation of endoparasite-of in which the parasite inhabits host cells. + + intracellular endoparasite of + + + + + + + + + inverse of intracellular endoparasite of + + has intracellular endoparasite + + + + + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + + co-roosts with + + + + + + + + + + + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + + + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + + + produced by + + + + + + + + + Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. + + represses expression of + + + + + + + + + Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. + + increases expression of + + + + + + + + + + A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + + is used to study + The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. + has role in modeling + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. + contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. + is preventative for condition + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + ameliorates condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + + A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. + exacerbates condition + + + + + + + + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. + condition ameliorated by + + + + + + + + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. + condition exacerbated by + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + + 2017-11-05T02:38:20Z + condition has genetic basis in + + + + + + + + + + + 2017-11-05T02:45:20Z + has material basis in gain of function germline mutation in + + + + + + + + + + + + + 2017-11-05T02:45:37Z + has material basis in loss of function germline mutation in + + + + + + + + + + + 2017-11-05T02:45:54Z + has material basis in germline mutation in + + + + + + + + + + + + 2017-11-05T02:46:07Z + has material basis in somatic mutation in + + + + + + + + + + + + 2017-11-05T02:46:26Z + has major susceptibility factor + + + + + + + + + + + 2017-11-05T02:46:57Z + has partial material basis in germline mutation in + + + + + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + + 2018-12-13T11:26:17Z + + has primary input or output + + + + + + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + + 2018-12-13T11:26:32Z + + has primary output + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + + 2018-12-13T11:26:56Z + + has primary input + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + + 2017-11-05T02:53:08Z + is genetic basis for condition + + + + + + + + + Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:55:51Z + is causal gain of function germline mutation of in + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:56:06Z + is causal loss of function germline mutation of in + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:56:40Z + is causal germline mutation in + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:57:07Z + is causal somatic mutation in + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. + + 2017-11-05T02:57:43Z + is causal susceptibility factor for + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. + + 2017-11-05T02:58:43Z + is causal germline mutation partially giving rise to + + + + + + + + + + + + 2017-11-05T03:20:01Z + realizable has basis in + + + + + + + + + + 2017-11-05T03:20:29Z + is basis for realizable + + + + + + + + + + + 2017-11-05T03:26:47Z + disease has basis in + + + + + + + + + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) + + 2017-11-05T03:29:32Z + disease has basis in dysfunction of + + + + + + + + + A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) + + 2017-11-05T03:37:52Z + disease has basis in disruption of + + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. + + 2017-11-05T03:46:07Z + disease has basis in feature + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. + + 2017-11-05T03:50:54Z + causal relationship with disease as subject + + + + + + + + + + + + + + + + + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) + + 2017-11-05T03:51:09Z + disease causes disruption of + + + + + + + + + + + + + disease causes dysfunction of (disease to anatomical entity) + + 2017-11-05T03:58:20Z + disease causes dysfunction of + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. + TODO: complete range axiom once more of CARO has been mireoted in to this ontology + This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. + + 2017-11-05T04:06:02Z + disease has location + + + + + + + + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity + + 2017-12-26T19:37:31Z + disease has inflammation site + + + + + + + + + + + + + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + + 2017-12-26T19:45:49Z + realized in response to stimulus + + + + + + + + + A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. + + 2017-12-26T19:50:53Z + disease has feature + + + + + + + + + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. + + 2017-12-26T19:58:44Z + disease arises from alteration in structure + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. + DEPRECATED inheres in + true + + + + + + + + DEPRECATED bearer of + true + + + + + + + + A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. + + has driver + + + + + + + + + + A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes. + + has disease driver + + + + + + + + + + + An interaction relationship wherein a plant or algae is living on the outside surface of another plant. + https://en.wikipedia.org/wiki/Epiphyte + epiphyte of + + + + + + + + + inverse of epiphyte of + + has epiphyte + + + + + + + + + + A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material + https://en.wikipedia.org/wiki/Kleptoparasitism + kleptoparasite of + + + + + + + + + inverse of kleptoparasite of + + kleptoparasitized by + + + + + + + + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. + creates habitat for + + + + + + + + + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. + ecologically co-occurs with + + + + + + + + + + An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + lays eggs on + + + + + + + + + inverse of lays eggs on + has eggs laid on by + + + + + + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + + has substance added + + + + + + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + + has substance removed + + + + + + + + + sardines 'immersed in' some 'oil and mustard' + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + + immersed in + + + + + + + + sardine has consumer some homo sapiens + + 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. + + has consumer + + + + + + + + + + bread 'has primary substance added' some 'flour' + + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. + + has primary substance added + + + + + + + + + + + + + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. + r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. + + + + + triggered by process + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit + + + + + triggered by process + RO:cjm + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + + regulates activity of + + + + + + + + + The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. + + regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. + + indirectly regulates activity of + + + + + + + + + The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. + +For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. + + decreases by repression quantity of + + + + + + + + + The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. + +For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. + + increases by expression quantity of + + + + + + + + + The entity A has an activity that directly positively regulates the quantity of B. + + directly positively regulates quantity of + + + + + + + + + The entity A has an activity that directly negatively regulates the quantity of B. + + directly negatively regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. + + indirectly activates + indirectly positively regulates activity of + + + + + + + + + AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) + An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. + + destabilizes quantity of + + + + + + + + + AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) + An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. + + stabilizes quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. + + indirectly inhibits + indirectly negatively regulates activity of + + + + + + + + + The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. + + directly regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. + + indirectly regulates quantity of + + + + + + + + + The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. + + indirectly negatively regulates quantity of + + + + + + + + + The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. + + indirectly positively regulates quantity of + + + + + + + + + + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg + 2020-04-22T20:27:26Z + has small molecule regulator + + + + + + + + + + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg + 2020-04-22T20:28:37Z + has small molecule activator + + + + + + + + + + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg + 2020-04-22T20:28:54Z + has small molecule inhibitor + + + + + + + + + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg + 2020-06-08T17:21:33Z + + + + acts on population of + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg + 2020-06-24T13:15:17Z + is small molecule regulator of + + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg + 2020-06-24T13:15:26Z + is small molecule activator of + + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg + 2020-06-24T13:15:35Z + is small molecule inhibitor of + + + + + + + + + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg + 2020-08-27T08:13:59Z + results in adhesion of + + + + + + + + + pg + 2021-02-26T07:28:29Z + + + + results in fusion of + + + + + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + + + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + + + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. + + 2020-07-17T09:26:52Z + has synaptic input or output in + has synaptic IO in region + + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. + + 2020-07-17T09:42:23Z + receives synaptic input in region + + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. + + 2020-07-17T09:45:06Z + sends synaptic output to region + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:52:19Z + has synaptic IO throughout + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:55:36Z + receives synaptic input throughout + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:57:27Z + sends synaptic output throughout + + + + + + + + + + + + + Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. + + 2020-07-20T12:10:09Z + has sensory dendrite location + has sensory terminal in + has sensory terminal location + has sensory dendrite in + + + + + + + + + + A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. + + 2021-05-26T08:40:18Z + receives synaptic input from neuron + + + + + + + + + A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. + + 2021-05-26T08:41:07Z + Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. + sends synaptic output to cell + + + + + + + + + A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. + + disease has infectious agent + + + + + + + + + + + + + + transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) + A relation between a material entity and some data in which the data is taken as exemplifying the material entity. + C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. + + This relation is not meant to capture the relation between occurrents and data. + has exemplar data + + + + + + + + + + exemplar data of + + + + + + + + + + A relation between a group and another group it is part of but does not fully constitute. + X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. + + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. + subcluster of + + + + + + + + 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1'). + transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3. + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + + + + + q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + different in magnitude relative to + + + + + q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + increased in magnitude relative to + + + + + q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + decreased in magnitude relative to + + + + + q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + similar in magnitude relative to + + + + + q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + has relative magnitude + + + + + + + + s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. + Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. + has cross section + + + + + s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + reciprocal of + + + + + q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') + A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. + + + has high plasma membrane amount + + + + + A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. + PMID:19243617 + + + + + + + + + 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') + A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. + + + has low plasma membrane amount + + + + + A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. + PMID:19243617 + + + + + + + + Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. + + 2021-11-05T17:30:14Z + has phenotype or disease + https://github.com/oborel/obo-relations/issues/478 + + + + + + + + + A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. + + 2021-11-05T17:30:44Z + has disease + https://github.com/oborel/obo-relations/issues/478 + + + + + + + + + X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. + ExO:0000083 + 2021-12-14T20:41:45Z + + has exposure medium + + + + + + + + + + + + A diagnostic testing device utilizes a specimen. + X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. + + + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08T12:00:00Z + utilizes + device utilizes material + + + + + + + + + Helper relation for OWL definition of RO:0018002 myristoylates + + is myristoyltransferase activity + + + + + + + + + + + + + + + A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input + + + myristoylates + + + + + + + + inverse of myristoylates + + myristoylated by + + + + + + + + + mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor + + is agonist of + + + + + + + + + + pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level + + is inverse agonist of + + + + + + + + + + tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level + + is antagonist of + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + + + + + Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. + + confers susceptibility to condition + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + + 2018-09-26T01:08:58Z + results in changes to anatomical or cellular structure + + + + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + + + + + + + + + + + + + Similarity that results from independent evolution. + + + homoplasous to + analogy + in homoplasy relationship with + + + + + + Similarity that results from independent evolution. + + + + + + + + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + ECO:0000075 + homocracous to + Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + in homocracy relationship with + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + + + + + + + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + analogy + Convergence usually implies a notion of adaptation. + in convergence relationship with + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + + + + + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + parallel evolution + Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + in parallelism relationship with + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + + + + + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + ECO:0000071 + MI:2163 + structural homologous to + idealistic homology + in structural homology relationship with + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by common descent. + + + homology + ECO:0000080 + RO_proposed_relation:homologous_to + SO:0000330 + SO:0000853 + SO:0000857 + SO:homologous_to + TAO:homologous_to + cladistic homology + historical homologous to + phylogenetic homology + taxic homology + true homology + in historical homology relationship with + + + + + + Homology that is defined by common descent. + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + ECO:0000067 + biological homologous to + transformational homology + Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + in biological homology relationship with + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + + + + + + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + atavism + rudiment + reversion + in reversal relationship with + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + + + + + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + + MeSH:Synteny + SO:0000860 + SO:0005858 + syntenic homologous to + synteny + in syntenic homology relationship with + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + MeSH:Synteny + + + + + + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + SO:0000854 + SO:0000859 + SO:paralogous_to + paralogous to + in paralogy relationship with + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + + + + + + + + + + + + + Paralogy that involves sets of syntenic blocks. + + + syntenic paralogous to + duplicon + paralogon + in syntenic paralogy relationship with + + + + + + Paralogy that involves sets of syntenic blocks. + + + DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y + + + + + + + + + + Syntenic homology that involves chromosomes of different species. + + + syntenic orthologous to + in syntenic orthology relationship with + + + + + + Syntenic homology that involves chromosomes of different species. + + + + + + + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + + fractional homology + partial homologous to + segmental homology + mixed homology + modular homology + partial correspondence + percent homology + in partial homology relationship with + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + ISBN:0123195837 + ISBN:978-0471984931 + + + + + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + MeSH:Structural_Homology,_Protein + protein structural homologous to + in protein structural homology relationship with + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + + + + + + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + + pseudogene + SO:non_functional_homolog_of + non functional homologous to + in non functional homology relationship with + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + SO:non_functional_homolog_of + + + + + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + ECO:00000060 + SO:0000855 + SO:0000858 + SO:orthologous_to + orthologous to + The term is sometimes also used for anatomical structures. + in orthology relationship with + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + + + + + + + + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + xenologous to + The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + in xenology relationship with + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + + + + + + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + + 1 to 1 homologous to + 1:1 homology + one-to-one homology + in 1 to 1 homology relationship with + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + BGEE:curator + + + + + + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + 1 to 1 orthologous to + 1:1 orthology + one-to-one orthology + in 1 to 1 orthology relationship with + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + + + + + + + + + + + Paralogy that results from a whole genome duplication event. + + + ohnologous to + homoeology + in ohnology relationship with + + + + + + Paralogy that results from a whole genome duplication event. + + + + + + + + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + in-paralogous to + inparalogy + symparalogy + in in-paralogy relationship with + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + + + + + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + alloparalogy + out-paralogous to + outparalogy + in out-paralogy relationship with + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + + + + + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + pro-orthologous to + in pro-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + + + + + + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + semi-orthologous to + The converse of pro-orthologous. + in semi-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + + + + + + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + serial homologous to + homonomy + in serial homology relationship with + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + + + + + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + + heterochronous homologous to + heterochrony + in heterochronous homology relationship with + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + ISBN:978-0674639416 + + + + + + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + juvenification + pedomorphosis + in paedomorphorsis relationship with + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + ISBN:978-0674639416 + + + + + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + in peramorphosis relationship with + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + + + + + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + in progenesis relationship with + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + ISBN:978-0674639416 + + + + + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + juvenilization + neotenous to + in neoteny relationship with + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + ISBN:978-0674639416 + + + + + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + mimicrous to + in mimicry relationship with + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + + + + + + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + 1 to many orthologous to + 1:many orthology + one-to-many orthology + co-orthology + many to 1 orthology + in 1 to many orthology relationship with + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + + + + + + + + + + + Historical homology that involves two members of a larger set of homologs. + + + many to many homologous to + many-to-many homology + many:many homology + in many to many homology relationship with + + + + + + Historical homology that involves two members of a larger set of homologs. + + + + + + + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + + 1 to many homologous to + one-to-many homology + 1:many homology + in 1 to many homology relationship with + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + BGEE:curator + + + + + + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + + apomorphous to + synapomorphy + in apomorphy relationship with + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + ISBN:978-0252068140 + + + + + + + + + + Historical homology that is based on distant shared ancestry. + + + plesiomorphous to + symplesiomorphy + This term is usually contrasted to apomorphy. + in plesiomorphy relationship with + + + + + + Historical homology that is based on distant shared ancestry. + + ISBN:978-0252068140 + + + + + + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + deep genetic homology + deep homologous to + generative homology + homoiology + Used for structures in distantly related taxa. + in deep homology relationship with + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + + + + + + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + hemiplasous to + in hemiplasy relationship with + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + + + + + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + gametologous to + in gametology relationship with + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + + + + + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + + MeSH:Chromosome_Pairing + chromosomal homologous to + in chromosomal homology relationship with + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + ISBN:0195307615 + + + + + + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + many to many orthologous to + many-to-many orthology + many:many orthology + trans-orthology + co-orthology + trans-homology + in many to many orthology relationship with + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + + + + + + + + + + + + Paralogy that involves genes from the same species. + + + within-species paralogous to + in within-species paralogy relationship with + + + + + + Paralogy that involves genes from the same species. + + + + + + + + + + + + Paralogy that involves genes from different species. + + + between-species paralogous to + The genes have diverged before a speciation event. + in between-species paralogy relationship with + + + + + + Paralogy that involves genes from different species. + + + + + + + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + post-displacement + in postdisplacement relationship with + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + + + + + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + in hypermorphosis relationship with + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + ISBN:978-0674639416 + + + + + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + synologous to + in synology relationship with + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + + + + + + + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + ECO:0000080 + isoorthologous to + in isoorthology relationship with + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + tandem paralogous to + iterative paralogy + serial paralogy + in tandem paralogy relationship with + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + ISBN:978-0878932665 + + + + + + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + apomorphic tendency + cryptic homology + latent homologous to + underlying synapomorphy + homoiology + homoplastic tendency + re-awakening + Used for structures in closely related taxa. + in latent homology relationship with + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + + + ISBN:0199141118 + + + + + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + generative homology + syngenous to + Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + in syngeny relationship with + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R + + + + + + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + 1:1 paralogy + apparent 1:1 orthology + apparent orthologous to + pseudoorthology + The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + in apparent orthology relationship with + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + + + + + + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + pseudoparalogous to + These genes may come out as paralogs in a single-genome analysis. + in pseudoparalogy relationship with + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + + + + + + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + equivalogous to + This may include examples of orthology, paralogy and xenology. + in equivalogy relationship with + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + interologous to + in interology relationship with + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + + + + + + + + + + + Similarity that is characterized by interchangeability in function. + + + functional similarity + in functional equivalence relationship with + + + + + + Similarity that is characterized by interchangeability in function. + + + + + + + + + + + + + Biological homology that involves parts of the same organism. + + + iterative homologous to + in iterative homology relationship with + + + + + + Biological homology that involves parts of the same organism. + + + + + + + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + duplicate xenology + multiple xenology + paraxenologous to + in paraxenology relationship with + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + + + + + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + plerologous to + This phenomenon is usually due to gene conversion process. + in plerology relationship with + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + + + + + + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + homotopous to + Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + in homotopy relationship with + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + + ISBN:0123195837 + + + + + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + heterotopy + in homeosis relationship with + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + + + + + + + + + + + + Synology that results from allopolyploidy. + + + homoeologous to + On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + in homoeology relationship with + + + + + + Synology that results from allopolyploidy. + + + + + + + + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + axis paramorphism + in paramorphism relationship with + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + + + + + + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + regulogous to + in regulogy relationship with + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + 100 + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + dos + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + PMID:24138933 + Wikipedia:Infant_mortality + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + continuant + Continuant + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + + + + + occurrent + Occurrent + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + + + s-region + SpatialRegion + BFO 2 Reference: Spatial regions do not participate in processes. + Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. + A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) + All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + spatial region + + + + + Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. + + per discussion with Barry Smith + + + + + A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) + + + + + + All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + + + + + + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + + + + + + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + + + + + + + + + + + + t-region + TemporalRegion + Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional + A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) + All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) + Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) + (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] + (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] + (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] + + temporal region + + + + + Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional + + per discussion with Barry Smith + + + + + A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) + + + + + + All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) + + + + + + Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) + + + + + + (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] + + + + + + (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] + + + + + + (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] + + + + + + + + + + + 2d-s-region + TwoDimensionalSpatialRegion + an infinitely thin plane in space. + the surface of a sphere-shaped part of space + A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) + (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] + + two-dimensional spatial region + + + + + A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) + + + + + + (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] + + + + + + + + + + st-region + SpatiotemporalRegion + the spatiotemporal region occupied by a human life + the spatiotemporal region occupied by a process of cellular meiosis. + the spatiotemporal region occupied by the development of a cancer tumor + A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) + All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) + Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) + Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) + Every spatiotemporal region occupies_spatiotemporal_region itself. + Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) + (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] + (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] + (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] + (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] + (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] + + spatiotemporal region + + + + + A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) + + + + + + All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) + + + + + + Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) + + + + + + Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) + + + + + + Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) + + + + + + (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] + + + + + + (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] + + + + + + (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] + + + + + + (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] + + + + + + (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition + + + + + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + + + + + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + + + + + + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + + + + + + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + + 0d-s-region + ZeroDimensionalSpatialRegion + A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) + (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] + + zero-dimensional spatial region + + + + + A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) + + + + + + (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] + + + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + quality + + + + + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + + + + + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + + + + + + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + + + + + + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + fiat-object-part + FiatObjectPart + or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 + the FMA:regional parts of an intact human body. + the Western hemisphere of the Earth + the division of the brain into regions + the division of the planet into hemispheres + the dorsal and ventral surfaces of the body + the upper and lower lobes of the left lung + BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions + b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) + (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] + + fiat object part + + + + + b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) + + + + + + (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] + + + + + + + + + + + 1d-s-region + OneDimensionalSpatialRegion + an edge of a cube-shaped portion of space. + A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) + (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] + + one-dimensional spatial region + + + + + A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) + + + + + + (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] + + + + + + + + + + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + object aggregate + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + + + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + + + + + + + + + 3d-s-region + ThreeDimensionalSpatialRegion + a cube-shaped region of space + a sphere-shaped region of space, + A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) + (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] + + three-dimensional spatial region + + + + + A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) + + + + + + (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] + + + + + + + + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + site + + + + + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + + + + + + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + + + + + + + + + object + Object + atom + cell + cells and organisms + engineered artifacts + grain of sand + molecule + organelle + organism + planet + solid portions of matter + star + BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. + BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). + BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 + BFO 2 Reference: an object is a maximal causally unified material entity + BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 + b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) + + object + + + + + b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + function + Function + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + function + + + + + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + + + + + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + + + + + + + + + p-boundary + ProcessBoundary + the boundary between the 2nd and 3rd year of your life. + p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) + Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) + (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] + (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] + + process boundary + + + + + p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) + + + + + + Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) + + + + + + (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] + + + + + + (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] + + + + + + + + + + + 1d-t-region + OneDimensionalTemporalRegion + the temporal region during which a process occurs. + BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). + A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) + (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] + + one-dimensional temporal region + + + + + A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) + + + + + + (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] + + + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + + + + + cf-boundary + ContinuantFiatBoundary + b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) + BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. + BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 + Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. + Every continuant fiat boundary is located at some spatial region at every time at which it exists + (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] + + continuant fiat boundary + + + + + b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) + + + + + + Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. + + + + + + (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] + + + + + + + + + + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + + immaterial entity + + + + + + + + + + + 1d-cf-boundary + OneDimensionalContinuantFiatBoundary + The Equator + all geopolitical boundaries + all lines of latitude and longitude + the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. + the median sulcus of your tongue + a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) + (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] + + one-dimensional continuant fiat boundary + + + + + a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) + + + + + + (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] + + + + + + + + + + + process-profile + ProcessProfile + On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels + One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. + The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. + b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) + b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) + (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] + (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] + + process profile + + + + + b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) + + + + + + b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) + + + + + + (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] + + + + + + (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] + + + + + + + + + + r-quality + RelationalQuality + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + a marriage bond, an instance of requited love, an obligation between one person and another. + b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) + (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] + + relational quality + + + + + b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) + + + + + + (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] + + + + + + + + + + 2d-cf-boundary + TwoDimensionalContinuantFiatBoundary + a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) + (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] + + two-dimensional continuant fiat boundary + + + + + a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) + + + + + + (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] + + + + + + + + + + 0d-cf-boundary + ZeroDimensionalContinuantFiatBoundary + the geographic North Pole + the point of origin of some spatial coordinate system. + the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet + zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. + a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) + (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] + + zero-dimensional continuant fiat boundary + + + + + zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. + + requested by Melanie Courtot + + + + + + a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) + + + + + + (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] + + + + + + + + + + 0d-t-region + ZeroDimensionalTemporalRegion + a temporal region that is occupied by a process boundary + right now + the moment at which a child is born + the moment at which a finger is detached in an industrial accident + the moment of death. + temporal instant. + A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) + (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] + + zero-dimensional temporal region + + + + + A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) + + + + + + (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] + + + + + + + + + + history + History + A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) + + history + + + + + A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) + + + + + + + + + + karlx + information content entity + + + + + + + + + karlx + Mexico City + + + + + + + + + karlx + + + + + + + + + karlx + UB philosophy department chair + + + + + + + + + karlx + + + + + + + + + karlx + + + + + + + + + karlx + + + + + + + + + karlx + minivan trunk + + + + + + + + + karlx + + + + + + + + + karlx + + + + + + + + + karlx + Bach's Well-Tempered Clavier + + + + + + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + relation has no temporal argument + + + + + + + + + + + + curation status specification + + + ready for release + + + + + pending final vetting + + + + obsolescence reason specification + + + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Project-3/Proj_3RO.properties b/Project-3/Proj_3RO.properties new file mode 100644 index 00000000..0cf2cc0f --- /dev/null +++ b/Project-3/Proj_3RO.properties @@ -0,0 +1,5 @@ +#Sun Mar 05 04:12:50 EST 2023 +jdbc.url= +jdbc.driver= +jdbc.user= +jdbc.password= diff --git a/Project-3/README.md b/Project-3/README.md deleted file mode 100644 index ea4be191..00000000 --- a/Project-3/README.md +++ /dev/null @@ -1,2 +0,0 @@ - -You know what's coming... diff --git a/Project-3/catalog-v001.xml b/Project-3/catalog-v001.xml new file mode 100644 index 00000000..6f94a99d --- /dev/null +++ b/Project-3/catalog-v001.xml @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/Project-3/proj_Q6.png b/Project-3/proj_Q6.png new file mode 100644 index 00000000..613874de Binary files /dev/null and b/Project-3/proj_Q6.png differ diff --git a/README.md b/README.md index dd6a0d78..dba97809 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # PHI-696 +VSCODE EDITING TEST + Artificial Intelligence communities have, for decades, worked to design computing systems able to solve complicated tasks as well as humans can. Siri, autonomous vehicles, Computer-Aided Diagnosing systems, and automated theorem provers, are examples of the fruits of such labor. For such feats of computing ingenuity to work properly, however, relevant knowledge must be represented in formalisms interpretable by computing systems. One goal of this course is to provide students with a deep understanding of formalisms underwriting contemporary knowledge representation. We will examine several ‘Description Logics’ which reflect decidable fragments of First-Order Logic and provide formal foundations for widely used semantic web languages. Semantic web languages – such as the Resource Description Framework – in turn provide concrete vocabularies used to represent information across the web. Another goal of this course is to provide students with a deep understanding of these semantic web languages, emphasizing their importance to the development of ontologies – structured vocabularies comprised of human and computer interpretable terminological content representing entities in some domain. Students will gain competency in the application of semantic web languages to represent the philosophical commitments of one of the most important ontologies in the world: Basic Formal Ontology (BFO).