the pathway links are predicates defined here
<https://docs.google.com/document/d/1R_AiCCRuWKI92JUCYXJRnKeYw-MiwKLR3kr9fJyYZfs/edit>.
the pathways are
DefineLink
DefinedPredicateNode "GO pathway term name"
AndLink
Predicate "protein relationship 1"
ProteinNode "x"
ProteinNode "y"
Predicate "protein relationship 2"
ProteinNode "y"
ProteinNode "z"
....
On Tuesday, August 8, 2017 at 11:00:54 AM UTC-7, Michael Duncan wrote:
>
> the AndLink semantics are for the simplified pathway representation for
> the current demo/toy bio-atomspace which only has binary links between
> proteins and abstracts out small molecules. so the pathway for the krebs
> cycle for instance is just directed links between the enzymes: ... ->
> isocitrate
> dehydrogenase -> alpha-ketoglutarate dehydrogenase -> Succinyl-CoA
> synthetase -> ...
>
> linus semantics look good for when the complete biopax pathway
> representation is translated into atomese.
>
> even then my intuition is that the AndLink semantics should be useful in
> pln inference about say the likelihood of a pathway being involved in
> distinguishing a case-control phenotype based on moses models of relative
> gene expression levels.
>
> On Monday, August 7, 2017 at 11:31:59 AM UTC-7, Ben Goertzel wrote:
>>
>> a pathway in biology is actually a network with directed arrows and
>> generally lots of loops.... there are even some hyperlinks e.g. for
>> catalysis... a pathway is a subhypergraph...
>>
>>
>>
>> On Aug 7, 2017 11:25, "Linas Vepstas" <linasv...@gmail.com> wrote:
>>
>>> no clue why its appropriate for biological pathways. Mike is designing
>>> that, not me.
>>>
>>> Anyway, a "pathway" is an ordered sequence where the ordering matters.
>>> Neither SetLink, nor AndLink are ordered. So if you actually want to have a
>>> path, i.e. a sequence of directed arrows, well .. you need to find a
>>> representation of biological pathways as directed arrows. But this is
>>> familiar ground, for opencog...
>>>
>>> --linas
>>>
>>> On Mon, Aug 7, 2017 at 1:21 PM, Ben Goertzel <b...@goertzel.org> wrote:
>>>
>>>> OK I get that... but I don't see why it is appropriate for biological
>>>> pathways...
>>>>
>>>> On Tue, Aug 8, 2017 at 2:19 AM, Linas Vepstas <linasv...@gmail.com>
>>>> wrote:
>>>> > First, lets review SetLink:
>>>> >
>>>> > SetLink
>>>> > ConceptNode "x"
>>>> > ConceptNode "y"
>>>> > ConceptNode "z"
>>>> >
>>>> >
>>>> > EquivalenceLink
>>>> > ConceptNode "last three letters of the alphabet"
>>>> > SetLink
>>>> > ConceptNode "x"
>>>> > ConceptNode "y"
>>>> > ConceptNode "z"
>>>> >
>>>> >
>>>> > MemberLink
>>>> > ConceptNode "x"
>>>> > ConceptNode "last three letters of the alphabet"
>>>> > MemberLink
>>>> > ConceptNode "y"
>>>> > ConceptNode "last three letters of the alphabet"
>>>> > MemberLink
>>>> > ConceptNode "z"
>>>> > ConceptNode "last three letters of the alphabet"
>>>> >
>>>> > Again, with TV's:
>>>> >
>>>> > MemberLink <1.0>
>>>> > ConceptNode "z"
>>>> > ConceptNode "last letters of the alphabet"
>>>> > MemberLink <0.9>
>>>> > ConceptNode "w"
>>>> > ConceptNode "last letters of the alphabet"
>>>> > MemberLink <0.8>
>>>> > ConceptNode "s"
>>>> > ConceptNode "last letters of the alphabet"
>>>> > MemberLink <0.2>
>>>> > ConceptNode "m"
>>>> > ConceptNode "last letters of the alphabet"
>>>> >
>>>> >
>>>> >
>>>> > Sooo .. AndMemberLink would be just like the above, except that
>>>> whereever
>>>> > you see SetLink above, you would have AndLink, and wherever you see
>>>> > MmeberLink above, you would have AndMemeberLink.
>>>> >
>>>> > --linas
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > On Mon, Aug 7, 2017 at 1:11 PM, Ben Goertzel <b...@goertzel.org>
>>>> wrote:
>>>> >>
>>>> >> I don't understand the proposed semantics of AndMemberLink, could you
>>>> >> explain?
>>>> >>
>>>> >>
>>>> >>
>>>> >> On Sat, Aug 5, 2017 at 1:07 AM, Michael Duncan <mjsd...@gmail.com>
>>>> >> wrote:
>>>> >> > i actually think an AndLink-like semantics better fits biochemical
>>>> >> > pathways
>>>> >> > at a computationally tractable level than partitions in that below
>>>> the
>>>> >> > level
>>>> >> > of a whole organism, where one pathway ends and another begins is
>>>> >> > largely
>>>> >> > arbitrary. also, if one link is missing then the whole thing
>>>> doesn't
>>>> >> > work
>>>> >> > but the last bit of a dead end might be the start of another path
>>>> that
>>>> >> > goes
>>>> >> > to the same place, more like words and phrases that can be
>>>> rearranged
>>>> >> > and
>>>> >> > swapped in different ways to say the same thing. linus idea of
>>>> >> > AndMemberLinks and OrMemeberLinks would get around the size
>>>> limitation
>>>> >> > and
>>>> >> > also seem like they would be useful for reasoning on moses models.
>>>> >> >
>>>> >> > On Monday, July 31, 2017 at 5:55:16 PM UTC-4, linas wrote:
>>>> >> >>
>>>> >> >> Hi Ben, Mike,
>>>> >> >>
>>>> >> >>
>>>> >> >> On Fri, Jul 21, 2017 at 9:41 PM, Ben Goertzel <b...@goertzel.org>
>>>> >> >> wrote:
>>>> >> >>>
>>>> >> >>> Some interesting representational issues have come up in the
>>>> context
>>>> >> >>> of Atomspace representation of pathways, which appear to have
>>>> more
>>>> >> >>> general implications…
>>>> >> >>>
>>>> >> >>> It seems the semantics we want for a biological pathway is sort
>>>> of
>>>> >> >>> like “the pathway P is a set of relationships R1, R2, …, R20” in
>>>> kinda
>>>> >> >>> the same sense that “the human body is a set of organs: brain,
>>>> heart,
>>>> >> >>> lungs, legs, etc.”
>>>> >> >>>
>>>> >> >>> First of all it seems what we have here is a part of
>>>> relationship…
>>>> >> >>> maybe
>>>> >> >>> we want
>>>> >> >>>
>>>> >> >>> PartLink
>>>> >> >>> ConceptNode “heart”
>>>> >> >>> ConceptNode “human-body”
>>>> >> >>>
>>>> >> >>> and
>>>> >> >>>
>>>> >> >>> PartLink
>>>> >> >>> >relationship<
>>>> >> >>> >pathway<
>>>> >> >>>
>>>> >> >>> PartLink and PartOfLink have come and gone in
>>>> >> >>> OpenCog/Novamente/Webmind history...
>>>> >> >>>
>>>> >> >>> An argument that PartLink should have fundamental status and a
>>>> >> >>> well-defined fuzzy truth value is given in this paper:
>>>> >> >>>
>>>> >> >>> https://www.academia.edu/1016959/Fuzzy_mereology
>>>> >> >>>
>>>> >> >>> However what we need for biological pathways and human bodies
>>>> seems
>>>> >> >>> like a bit more. We want to say that a human body consists of a
>>>> >> >>> certain set of parts... not just that each of them is a part...
>>>> We're
>>>> >> >>> doing a decomposition.
>>>> >> >>>
>>>> >> >>> One way to do this would be
>>>> >> >>>
>>>> >> >>> PartitionLink
>>>> >> >>> ConceptNode “human-body”
>>>> >> >>> ListLink
>>>> >> >>> ConceptNode “legs”
>>>> >> >>> ConceptNode “arms”
>>>> >> >>> ConceptNode “brain”
>>>> >> >>> etc.
>>>> >> >>>
>>>> >> >>> Relatedly, we could also have
>>>> >> >>
>>>> >> >>
>>>> >> >> As mentioned earlier, there are several problems with this
>>>> format. One
>>>> >> >> is
>>>> >> >> the "oops I forgot to mention xyz in the list" or "gosh I should
>>>> have
>>>> >> >> left
>>>> >> >> out pqr" and this becomes a big problem: you have to delete the
>>>> >> >> PartitionLink, delete the ListLink, create a new list and
>>>> partition.
>>>> >> >> In the
>>>> >> >> meanwhile, some other subsystem might be holding a handle to the
>>>> old,
>>>> >> >> now-wrong PartitionLink, and there is no effective way of
>>>> announcing
>>>> >> >> "hey
>>>> >> >> stop using that old thing, get my new thing now".
>>>> >> >>
>>>> >> >> A second problem is that the above doesn't have anywhere to hang
>>>> >> >> addtional
>>>> >> >> data: e.g. "legs are a big part of the human body, having a mas of
>>>> >> >> nearly
>>>> >> >> half of the body." You can't just slap that on as a (truth)value,
>>>> cause
>>>> >> >> there's no where to put that value.
>>>> >> >>
>>>> >> >> Third problem is that large list-links are hard to handle in the
>>>> >> >> pattern
>>>> >> >> matcher. Its much much harder to write a query of the form "find
>>>> me
>>>> >> >> all
>>>> >> >> values of $X where
>>>> >> >>
>>>> >> >> PartitionLink
>>>> >> >> ConceptNode “human-body”
>>>> >> >> ListLink
>>>> >> >> ConceptNode “legs”
>>>> >> >> VariableNode “$X”
>>>> >> >> ConceptNode “brain”
>>>> >> >>
>>>> >> >> because, ... well the ListLink is an ordrerd link, not an
>>>> unordered
>>>> >> >> link.
>>>> >> >> If you forget to include the pqr (added above) then the search
>>>> will
>>>> >> >> fail.
>>>> >> >> You could try to use unordered links and globnodes, but these
>>>> lead to
>>>> >> >> other
>>>> >> >> difficulties, including the n! possible permutations of an
>>>> unordered
>>>> >> >> link
>>>> >> >> become large n-factorial large when the unordered link has n
>>>> items in
>>>> >> >> it.
>>>> >> >> Recall that old factorial-70 trick used to make calculators
>>>> overflow.
>>>> >> >>
>>>> >> >> In general, any link with more than 3 or 4 or 5 items in it is bad
>>>> >> >> news.
>>>> >> >> This is a generic statement about knowledge representation in
>>>> opencog.
>>>> >> >>
>>>> >> >>
>>>> >> >>> OverlappingPartitionLink
>>>> >> >>> C
>>>> >> >>> L
>>>> >> >>>
>>>> >> >>> if we want to encompass cases where the partition elements in L
>>>> can
>>>> >> >>> overlap; or
>>>> >> >>>
>>>> >> >>> CoveringLink
>>>> >> >>> C
>>>> >> >>> L
>>>> >> >>>
>>>> >> >>> if we want to encompass cases where the partition elements in L
>>>> can
>>>> >> >>> overlap, AND the elements in L may encompass some stuff that’s
>>>> not in
>>>> >> >>> C
>>>> >> >>>
>>>> >> >>> For the pathway case, we could then say
>>>> >> >>>
>>>> >> >>> PartitionLink
>>>> >> >>> ConceptNode “Krebs cycle”
>>>> >> >>> ListLink
>>>> >> >>> >relationship 1<
>>>> >> >>> >relationship 2<
>>>> >> >>> etc.
>>>> >> >>>
>>>> >> >>>
>>>> >> >>> Now this solves the semantics problem but doesn’t solve the
>>>> problem of
>>>> >> >>> having a long ListLink…. A biological pathway might have 100s or
>>>> >> >>> 1000s of relationships in it, and we don't usually want to make
>>>> lists
>>>> >> >>> that big in the Atomspace...
>>>> >> >>>
>>>> >> >>> To solve this we could do something like (for the human body
>>>> case)
>>>> >> >>>
>>>> >> >>> PartitionLink
>>>> >> >>> ConceptNode “human-body”
>>>> >> >>> PartitionNode “body-partition-1”
>>>> >> >>>
>>>> >> >>> PartitionElementLink
>>>> >> >>> PartitionNode “body-partition-1"
>>>> >> >>> ConceptNode “legs”
>>>> >> >>>
>>>> >> >>> PartitionElementLink
>>>> >> >>> PartitionNode “body-partition-1"
>>>> >> >>> ConceptNode “arms”
>>>> >> >>>
>>>> >> >>> etc.
>>>> >> >>>
>>>> >> >>> and similarly (for the biological pathway case)
>>>> >> >>>
>>>> >> >>> PartitionLink
>>>> >> >>> ConceptNode “Krebs cycle”
>>>> >> >>> PartitionNode “krebs-partition-1”
>>>> >> >>>
>>>> >> >>> PartitionElementLink
>>>> >> >>> PartitionNode “krebs-partition-1"
>>>> >> >>> >relationship 1<
>>>> >> >>>
>>>> >> >>> PartitionElementLink
>>>> >> >>> PartitionNode “krebs-partition-1”
>>>> >> >>> >relationship 2<
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >> Yeah, sure. Not sure why the existing MemberLink is not
>>>> sufficient for
>>>> >> >> your purposes. The MemberLink has reasonably-well-defined
>>>> semantics,
>>>> >> >> there
>>>> >> >> are already rules for handling it in PLN (or there will be rules
>>>> -- I
>>>> >> >> think
>>>> >> >> its something Nil has thought about) I'm not clear on why you'd
>>>> want
>>>> >> >> to
>>>> >> >> invent something that is just like MemberLink but is different.
>>>> >> >>
>>>> >> >>>
>>>> >> >>>
>>>> >> >>> ...
>>>> >> >>>
>>>> >> >>> There could be some nice truth value math regarding these, e.g.
>>>> we
>>>> >> >>> could introduce Ellerman's "logical entropy" which is really a
>>>> >> >>> partition entropy. There are also connections with some recent
>>>> >> >>> theoretical work I've been doing on "graphtropy" (using
>>>> "distinction
>>>> >> >>> graphs" that generalize partitions), which I'll post a paper on
>>>> >> >>> sometime in the next week or two.... But that will be another
>>>> email
>>>> >> >>> for another day...
>>>> >> >>
>>>> >> >>
>>>> >> >> Yeah graphical-entropy is something that I keep trying to work on,
>>>> >> >> except
>>>> >> >> that every new urgent disaster of the day distracts me from it.
>>>> >> >>
>>>> >> >> --linas
>>>> >> >>>
>>>> >> >>>
>>>> >> >>> -- Ben
>>>> >> >>>
>>>> >> > --
>>>> >> > You received this message because you are subscribed to the Google
>>>> >> > Groups
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>>>> send
>>>> >> > an
>>>> >> > email to opencog+u...@googlegroups.com.
>>>> >> > To post to this group, send email to ope...@googlegroups.com.
>>>> >> > Visit this group at https://groups.google.com/group/opencog.
>>>> >> > To view this discussion on the web visit
>>>> >> >
>>>> >> >
>>>> https://groups.google.com/d/msgid/opencog/e1df7273-da14-45f5-8d0d-5ebad0d31217%40googlegroups.com
>>>> .
>>>> >> >
>>>> >> > For more options, visit https://groups.google.com/d/optout.
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >> Ben Goertzel, PhD
>>>> >> http://goertzel.org
>>>> >>
>>>> >> "I am God! I am nothing, I'm play, I am freedom, I am life. I am the
>>>> >> boundary, I am the peak." -- Alexander Scriabin
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> Ben Goertzel, PhD
>>>> http://goertzel.org
>>>>
>>>> "I am God! I am nothing, I'm play, I am freedom, I am life. I am the
>>>> boundary, I am the peak." -- Alexander Scriabin
>>>>
>>>
>>>
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