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Alan Ruttenberg › Comments
emotion occurrent: John is angry, doesn't have to know it
- Melanie
emotion disposition (to undergo emotion occurrent if right circumstances): John has been angry with Mary for 3 weeks
- Melanie
emotional personality trait: John is an angry person. Characteristic of a person involving a predisposition
- Melanie
MC: is 'cognitive representation' a term submission for BFO?
- Melanie
Not clear why appraisal process is a necessary part of emotion occurent
- steschu
I think a cognitive representation is just a sort of quality. There won't be a corresponding GDC because you can't transfer it.
- Colin Batchelor
Colin, not only qualities - perhaps processes - think dram
- Alan Ruttenberg
@Alan - yeah, meant to say "just things that are already in BFO like qualities" - didn't mean to exclude processes or dispositions!
- Colin Batchelor
in CAO (COG analysis ontology): new relation 'denoted_by' not inverse of iao:denotes. Unclear as why this is the case to me?
- Melanie
Supports ontoCOG, under the Ontobat umbrella (that's a lot of onto- ;))
- Melanie
denoted_by sounds dodgy to me---Cambridgy.
- Colin Batchelor
pointer to CAO?
- Alan Ruttenberg
Stefan asked the same question re denoted_by, and she was explaining (I hope I got it right) that she is trying to link a material entity to a GO ID, but as the same GO ID may denote several mat entities it didn't work.
- Melanie
Maybe confusion between class2class relations with instance2instance relations
- steschu
Talk: OWL-DL Ontology for Classification of Lipids: Hong-Sang Low
Meena Kharatmal, Frank and Melanie liked this
Semantic integration is necessary for lipid research, but no single unified, consistent and universally accepted lipid classification system is there.
- Robert Hoehndorf
Objective: formalize lipid nomenclature and classification using OWL-DL.
- Robert Hoehndorf
Based on BFO as top-level, but mainly reuse the Independent continuant category.
- Robert Hoehndorf
Chebi not suitable: not all relationships from ChEBI are relevant, lack of formal consistency
- Robert Hoehndorf
Compound has-part Organic_group AND Organic_group part-of Compound
- Robert Hoehndorf
34 additional properties of the has-part-X kind to specify number restrictions which do not work with transitive (has-part) relations
- Robert Hoehndorf
"Added additional properties to enable cardinality constraints" - sounds like not QCR aware - probably should be fixed for OWL 2 version to use fewer properties. Re transitive issue, they still don't need so many properties.
- Alan Ruttenberg
Ah - future works mentions QCR :)
- Alan Ruttenberg
So, the discussion is exactly about QCRs together with transitive properties.
- Robert Hoehndorf
Wondering if anyone has a good definition of "functional group"
- Alan Ruttenberg
@alan: As a very very rough first draft, functional groups are those special parts of molecules that ground (or maybe their structures, which are qualities, ground) dispositions. At least that's what I argued in my tutorial.
- Colin Batchelor
It would have to be some very special dispositions: the disposition to be attracted by gravity would not belong there. Do you have a way of saying which dispositions are grounded there?
- Robert Hoehndorf
@leechuck "some very special dispositions" - yes, those which are realized as processes of bond breaking or bond formation, roughly. (Sorry, missed this at the time.)
- Colin Batchelor
http://www.biomedcentral.com/1471-21... - Prototype Semantic Infrastructure for Automated Small Molecule Classification and Annotation in Lipidomics. Just came out
- Melanie
Neurolex and NIF, Jeff Grethe
NIF registry -- doesn't INCF have a registry also -- what's the relationship?
- Phil Lord
multiple formats -- is that going to cause them a headache?
- Phil Lord
No comments on Jeff's stuff? Has everyone lost network?
- Phil Lord
I have poked Jeff to join this discussion
- Alan Ruttenberg
Community involvement via wiki approach.
- dosumis
The wiki is a 'lexicon' not a '-pedia' [new distinction to me] - in that it is for recording distinguishing properties, not everything that we know about instances of some particular class - e.g.- cerebellum. [My take: I don't think there is any clean distinction here. Distinguishing properties defined comparatively and relative to the classifications needed. If types of useful classificating expand, what is now considered '-pedia' might later become key distinguishing properties.]
- dosumis
Wiki has nice feature of allowing properties to be chosen from a pick-list, populated appropriately dependent on parent class
- dosumis
We do distinguish between dictionaries and encyclopedias. Dictionaries, and I consider the lexicon to be a form of dictionary, concentrate on definitions and provide things like synonyms, variants. What I wanted for the Neurolex was to provide an easy way to look up the meaning of the term for the purposes of data annotation, so it concentrates on defining criteria. Wikipedia is a place to go if you want to learn about the history of a concept, who says what about it, etc.
- Maryann Martone
Panel Session
Is SPARQL easier than SOAP?
- Phil Lord
community driven annotation is good, but how do we keep the annotation accurate
- Phil Lord
sparql: sort of like teaching a man to fish versus giving him a meal
- Alan Ruttenberg
Semantic Web for Neuroscience, Alan Ruttenberg
Semantic Web builds on the web
- Phil Lord
a virtue of the web seemless connection from inside to outside organizations
- dosumis
Oops, duplicate rooms...
- Phil Lord
Yeh - let's just use this one.
- dosumis
Semantic Web for network effects
- Phil Lord
www developed so rapidly in part because all could view source, and use this to generate their own web pages in simple html - semantic web equivalent = ???
- dosumis
Good question -- but then semantic web built on top of web -- not trying to replace this
- Phil Lord
Obvious simple examples RSS or friend of a friend
- Phil Lord
Now is that SPARQL query a good example of how easy it can all be?
- Phil Lord
no - shows Allan brain example of cleaner front end for this
- dosumis
Some of the mash up's can be really good -- SW technology is more geeky than base WWW; but geeks can build stuff for normal humans also.
- Phil Lord
Take home message - Breaking down terms into their components is key to getting this stuff to work - peptide neurotransmitter examples show this clearly.
- dosumis
Take home message2 - to ge the most out of ontology building, you need to share your ontology and re-use other people's open ontologies.
- dosumis
url: http://www.russet.org.uk/blog... live blog
- Phil Lord
Gully's question: How do you get biologists to think in this way?
- dosumis
Think that some biologists already do. Nothing wrong starting small.
- Phil Lord
Alan's reply to Gully: 1. Make sure the text definitions are clear to non-experts. 2. Biologists shouldn't need to interact with the geeky ontology representation. Need interfaces over this that are clear to them. Some examples in work Neuro-commons
- dosumis
My slides: http://ashby.csail.mit.edu/present...
- Alan Ruttenberg
"Now is that SPARQL query a good example of how easy it can all be?" :)
- Alan Ruttenberg
No - it's an example that it's possible to do something useful with SPARQL, even something that, as far as I know, isn't possible without a lot harder work in other systems.
- Alan Ruttenberg
Suggestion to involve biologists at large meetings: move a semantic-web description of individual poster/talk to the name tag. The description itself can be requested at the time of abstract submission from the authors & viewers of pre-meeting abstracts
- Pavan Ramkumar
the trouble with semantics: from a Chinese Enclyclopedia: http://novelvig.blogspot.com/2009... #incf09
this isn't a problem -- it's a precise statement of a classification. It might be a bad classification, but it's testable now that it's been explicitly stated
- Phil Lord
what's missing: No definitions of the terms. No criteria for deciding whether the classification is good. In science, we can and should create questions, retrieving answers to which *should* be enabled by our ontologies, and then reject or fix ontologies that don't perform.
- Alan Ruttenberg
agreed -- but again, you can see that there are no definitions because they have explictly stated their classification. Explicit bad is much better than implicit bad
- Phil Lord
l. et cetera
- Alan Ruttenberg
is "animals are divided into" explicit or implicit expression of disjointness among classes?
- Alan Ruttenberg
if there *is* the disjoint, then the ontology is inconsistent afaik
- Alan Ruttenberg
sure, that's true, it's a bit of a mess
- Phil Lord
Is refusing to watch dirty dancing
@Frank - dude I'm watching it and trying to classify OBI's ontie merge. 100% chance of seeing Swayze's arse - how is that a bad thing. You don't get that with ontologies.
- Helen Parkinson
from email
deal, see if you can classify in 3.4 - out of memory and it has ALL the memory. Now trying with 4 and max heap. Ontie had better be good. I may need to get out more.
- Helen Parkinson
from email
P4 x pellet = null pointer exception, lovely.
- Helen Parkinson
from email
I thought we had a policy of, don't commit if it does not reason?
- Frank
@frank - well it does for Alan, some of the time. Roll back's an option, so far I've not classified it in 3/4 - don't know if anyone else has tried.
- Helen Parkinson
from email
setting it up on a faster machine, if I can work out how to use a swiss keyboard - getting there...
- Frank
null pointer exception for pellet and fact in 4. joy.
- Helen Parkinson
from email
"she was with him in his room all night".....damn it hurray up and download
- Frank
@frank - no-one puts frank in a corner
- Helen Parkinson
from email
@frank - oh no swayze sunday - have you got a shed mate?
- Helen Parkinson
from email
nope, she is away at a conference so I will get peace to watch it - I mean wont have to watch it
- Frank
Ok, I give in, can't be classified on my laptop.
- Helen Parkinson
from email
progress bar shows half way - painfully slow...
- Frank
passed consistency, up to 1h 30 minutes for infering hierarchy, did not finnish - gave up
- Frank
both Helen and Bjoern succeeded. Check your kit.
- Alan Ruttenberg
works for me too - pellet 2.0 in P4 and cmd line. pellet 1.5 doesn't succeed P3 or cmd line. To cheer you up, I'll bring the dirty dancing DVD for next meeting :)
- Melanie
AT&T: How is it possible that I can't get 3G everywhere in San Francisco. And that edge sucks so bad as backup?
@Alan Ruttenberg <http://friendfeed.com/alanrut...> which part of vacation do you not understand?
- Helen Parkinson
from email
Paper maps obsoleted by iPhone ... As long as there is a network connection. That said, it's alway a struggle :)
- Alan Ruttenberg
from email
Talk: A unified ontological-semantic substrate for physiological simulation and cognitive modeling: Sergei Nirenburg
Frank, Allyson Lister, Helen Parkinson and 3 other people liked this
goal: simulate physiological processes, model human cognitive capabilities, support automatic tutoring, integrate into society of intelligent agents
- Robert Hoehndorf
agent has body + mind
- Robert Hoehndorf
technical term: "who did what to whom"
- Alan Ruttenberg
this is hot stuff
- Alan Ruttenberg
I wonder why they don't use situation theory
- Robert Hoehndorf
Showing how the lexicon represents multiple senses of words
- Alan Ruttenberg
Demo of their system will be up during the break.
- Robert Hoehndorf
system represents process of learning by people - "inescapable"
- Alan Ruttenberg
Impressive!
- Michel Dumontier
The challenge - get them to open up their work.
- Alan Ruttenberg
Pierre Lindenbaum, Robert Hoehndorf, dosumis and Michel Dumontier liked this
The CRAFT corpus: manually annotated text corpus as resource for bio NLP community - aimed to be used as gold standard
- Melanie
Semantic annotation using all terms of selected OBOs, GO CC, Celle type, NCBI tax and Chebi
- Melanie
difficulty determining essential information about referent from context - e.g. is complex being referred to (->GOcc) or not.
- dosumis
Knowtator: tool for manual annotation (http://knowtator.sourceforge.net/)
- Melanie
GO BP and MF: somewhat ambiguous state (eg regulation of transcription and transcription regulator)
- Melanie
Can be v. difficult to decide whether GO BP or MF is referent. [Note - this fits with my own experience]
- dosumis
3rd issue: Non canonical, pathological and ex-vivo entities and processes: often non-canonical can only be inferred if reading carefully paper -> their policy is to annotate everything
- Melanie
"George Bush attacked Iraq". By the reasoning proposed re: MF and BP, we should remove the distinction people with military units, because it is hard, from a textual mention, to determine whether we mean George Bush the person, or George Bush as a name for the armed forces of the United States.
- Alan Ruttenberg
verb nominalizations (eg "formation") can be continuants or occurrents -> when one possible reading is occurrent that is what they keep
- Melanie
Processes and functions are not the same sorts of things. Functions (in the MF sense) inhere in particular molecules. Their realizations typically involve multiple proteins - no phoshorylation process without 1) Bearer of a kinase function, 2) ATP, 3) a molecule which receives the modification. An *instance* of the process depends on 3 things. An *instance* of the function depends on 1.
- Alan Ruttenberg
General conclusion - ambiguities of text regarding fundamental BFO distinctions (continuant v continuant; process vs function) => the need for heuristics to => inter-annotator consistency.
- dosumis
@Alan: the distinction of processes and functions is important. could you please direct me as to where i can find more details about it.
- Meena Kharatmal
I will record for posterity the mea culpa part of the question and answer that followed - the documentation of ontologies and and instructions for how to think about and use them is inadequate and fixing that should be a challenge for all ontologists and in particular the OBO Foundry
- Alan Ruttenberg
From questions: Heated discussion of how to deal with this issue. Alan Ruttenburg: - better documentation. Alan Rector - We need to improve the ontologies so that the we can annotate where there is ambiguity (? My interpretation of his comment. May not have captured it well)
- dosumis
@Meena, a reasonable place to start would be http://ontology.buffalo.edu/smith... if you haven't already read that. I will find some other more specific references
- Alan Ruttenberg
Banana, banana banana and banana banana banana. Not to mention banana or indeed banana. See my tutorial.
- Colin Batchelor
@Meena, http://ontology.buffalo.edu/bio... too
- Alan Ruttenberg
banana
- Alan Ruttenberg
@Colin - when are you giving it next. Or do you mean see the slides from your tutorial ;-) (Where are they) - Here's mine: http://ashby.csail.mit.edu/present...
- Alan Ruttenberg
@alan, sorry: http://icbo.buffalo.edu/present...
- Colin Batchelor
@Alan: thanx a ton for the references and also for your slides.
- Meena Kharatmal
@Colin: thanx, the tutorial has information on processes, functions, role, etc.
- Meena Kharatmal
Talk: Cross-product extensions to the Gene Ontology: Chris Mungall
GO primarily used for humans
- Robert Hoehndorf
Problems: maintenance and errors by combinatorial terms and tangled polyhierarchies
- Robert Hoehndorf
Solution: normalization + reasoning
- Robert Hoehndorf
Logical definition structure:An X is a G that D
- Robert Hoehndorf
Necessary and sufficient conditions that mirror text definition
- Robert Hoehndorf
Expressivity: equivalence axioms between named classes and positive conjunctions of named class and one or more existential restrictions
- Robert Hoehndorf
There is (or seems to be) an OBO principle of "positivity"
- Robert Hoehndorf
Mitochondrial translation =def translation that occurs_in mitochondrion
- Robert Hoehndorf
13k classes have provisional logical definitions (46% of all classes)
- Robert Hoehndorf
Uberon: multi-species anatomy ontology - current ontolgoies are species-specific
- Melanie
Implicit multi-species anatomy ontology taken out, now called the Uberon anatomy ontology
- Robert Hoehndorf
uberon for metazao - they won't cover plants for example, too different
- Melanie
segmentation, chebi slim, RDBMS reasoning to prevent issues with reasoners not scaling size-wise
- Melanie
inferred superclasses are asserted (did I get that right?)
- Melanie
not sure that the claim about not being able to reason in-memory on these is true any more
- Alan Ruttenberg
"uberon for metazao - they won't cover plants for example, too different". Only metazoans huh, not too ambitious then...
- dosumis
Talk: Modeling neurons and neuronal properties in the senselab ontology: Matt Holford
Frank liked this
Senselab is a collection of databases defining neurological terms and categorizing current research using these terms.
- Robert Hoehndorf
SLNO Class Structure: SLObject is the base, has_description, has_name, has_id are common properties
- Robert Hoehndorf
Matt needs to connect more with other work in his field (I told him same in person :)
- Alan Ruttenberg
Talk: Concepts, Modeling and Confusion: Harold Solbrig
Melanie liked this
I hope he will talk about unicorns :)
- Robert Hoehndorf
Use of "concept" was the cause of endless confusion
- Robert Hoehndorf
Correct solution is getting rid of the use of "concept"
- Robert Hoehndorf
You have succeeded when people stop to argue what names to model, but rather to argue about the names for the stuff you modelled
- Robert Hoehndorf
rename "unicorn", "unicorn description"
- Alan Ruttenberg
@Alan: no, I hoped it to be about /unicorns/. You know, these animals which are white and have a huge horn on their head :)
- Robert Hoehndorf
@robert, no, I don't know ;-)
- Alan Ruttenberg
Then what do you represent in a unicorn represention? :)
- Robert Hoehndorf
an idea - an element of second order reality
- Alan Ruttenberg
I don't get different orders of reality, I think there is only one reality. And there is the idea of "unicorn", and there is /Unicorn/, which does not have instances: unicorn the horse-like animal with a big horn :)
- Robert Hoehndorf
ideas can about first order reality, but we also have the capacity for them to reorder those elements to make combinations that are not in first order reality
- Alan Ruttenberg
yay! unicorns
- Chris Mungall
I missed them :)
- Melanie
there is one reality, but there are many parts and classes of such parts
- Alan Ruttenberg
Harold: there is no referent in the case of unicorn, only thought
- Melanie
Werner's classification: First order reality = what you have before you have things like brains. Second order reality: things that brains have. Third order reality: information artifacts created by brain bearers.
- Alan Ruttenberg
@melanie: there is a referent of unicorn, a thought ;-)
- Alan Ruttenberg
I see, so these are just three kinds of things in one reality; I find it very unfortunate to call it layers on reality, though.
- Robert Hoehndorf
Werner calls it "order" not "layer"
- Alan Ruttenberg
@Alan: actually, there is no referent of "Unicorn", because there are none (as far as I can tell). I can only make this statement and it has meaning when I know the meaning of "unicorn". And this is what an ontology should provide me with.
- Robert Hoehndorf
@Robert: Perhaps there is no *intended* referent. However, given that I take that all information artifacts are in a dependence relation to something in reality, there is something that "unicorn" corresponds to. Perhaps we will agree to not call that relation "reference". But there is *some* relation.
- Alan Ruttenberg
Harold has more levels of reality than Werner
- Chris Mungall
@Alan: but my statement "There are no unicorns" - which I believe is a true statement - is only true, if unicorn refers to the animal: there very obviously are unicorns in our minds, this conference is a proof of that :)
- Robert Hoehndorf
@Robert, if there are unicorns in our mind, then there are horses in our mind. Note however, that these "horses" are not the ones that run around outside, lest our heads be too heavy to lift.
- Alan Ruttenberg
unicorn!
- Chris Mungall
@Alan: and both these horses and unicorns - in our mind - exist: but the statement "there is a unicorn in this room" is false only if "unicorn" refers to the horse-like animal. If "unicorn" refers to ideas, there are many unicorns in this room - a statement I would not like to accept easily.
- Robert Hoehndorf
@Robert: Please define "refers". Then I will be able to see if I understand what you mean.
- Alan Ruttenberg
unicorn drinking game anyone?
- Chris Mungall
Sorry, there is free booze coming up, I suggest we continue over beer and post the summary here - if we can remember tomorrow ;)
- Robert Hoehndorf
I concur :)
- Alan Ruttenberg
@Rob: do you believe in round squares?
- Chris Mungall
@Chris: no, round squares are inconsistent classes, they could not have an instance in any possible world.
- Robert Hoehndorf
Talk: The RNA Ontology: Neocles Leontis
Need to account for RNAs in an ontology,capture structures, homology, function
- Robert Hoehndorf
objectives: integrate diverse data regarding 3D and sequence data, describe structues, align homologuous molecules, draw new inferences regarding RNA structure, evolution and function
- Robert Hoehndorf
closest relations: BFO, Relation Ontology, SO, ChEBI, Go
- Robert Hoehndorf
First challenge ist a classification of base-pairs
- Robert Hoehndorf
In addition to base-pairing is base-stacking, then base-backbone interactions
- Robert Hoehndorf
Future research: align with BFO, integrate with SO, ChEBI, GO
- Robert Hoehndorf
Future research: formalize relations, develop axioms for describing interaction relations
- Robert Hoehndorf
Checked out the google code group - lots of file releases, but not sure why they aren't using the subversion repository for them - ah here: http://rnao.googlecode.com/svn...
- Alan Ruttenberg
@alan, we've only been using the subversion repository as of last week. But that was only because I couldn't work out how to get svn to work.
- Colin Batchelor
dosumis, Meena Kharatmal and Frank liked this
Is Robert real? Or is he a conceptualization of a particular view of the world?
- Alan Ruttenberg
Our task is to create a formal specification that is true in our domain as they supply the meaning for the terms.
- Alan Ruttenberg
Discussing sequences as actual molecules - the first sense
- Alan Ruttenberg
Now sequences as some sort of syntactic entities. Here a junction is the adjacency of two symbols
- Alan Ruttenberg
not all sequences are sequences of molecules
- Alan Ruttenberg
Third sense - abstract information bearing entities - independent of space and time. There is a sequence and it can have multiple tokens. "AC" and "AC" (tokens) in "ACAC" represent the same sequence.
- Alan Ruttenberg
(my thought - the independent from space and time part bugs me :) )
- Alan Ruttenberg
Now explains his axiomatization
- Alan Ruttenberg
unfortunately I don't get why having different senses is an issue :(
- Melanie
@melanie, because different things are true of different senses
- Alan Ruttenberg
@alan - yes - and what prevents you from using the one you actually want/need? If I want to talk physical properties I will consider the material entity one. I would think it depends on which aspect you want to model, providing there is a way to relate different views of the same thing.
- Melanie
@melanie, absolutely - the problem only occurs when there are not different types defined and instead a single term is used to denote all the senses.
- Alan Ruttenberg
@alan: I see! Thanks :)
- Melanie
robert: i would be interested to see the slides of your talk
- Meena Kharatmal
@Meena: you can find my slides on http://lc2.eu/talks...
- Robert Hoehndorf
@Robert: Thanks for the slides. It was really interesting to browse the slides.
- Meena Kharatmal
I think the weak supplementation axiom holds for *instances* of generically dependent continuants. Robert's conclusions apply to GDC types.
- Chris Mungall
@Chris: Can you please elaborate a bit? I intended to talk about the instances, and I believe it does not hold for the instances of GDCs (already because I don't think ontological categories can have parts), but I would love to see why I am wrong. My example is the sequence ACA. There are several GDCs which are exemplified by ACA: A GDC that is exemplified by all ACAs, one for all ACs,...
more...
- Robert Hoehndorf
Talk: Evolution of the Sequence Ontology terms and relationships: Karen Eilbeck
SO is used for genome annotation, in model organism databases (Chado) and the GFF3 file format)
- Robert Hoehndorf
used for browsing (Gbrowse), protein feature annotation - biosapiens, nlp by the RSC
- Robert Hoehndorf
SO is needed to structure and annotate genomic sequence data
- Robert Hoehndorf
SO annotators want to annotate the "reality of the assembly"
- Robert Hoehndorf
Change: new Aristotelian definitions (textual), eliminate orphan terms, use All-Some relations between universals
- Robert Hoehndorf
Sequence features are generically dependent continuants - means: more than 1 bearer and it can be transferred.
- Robert Hoehndorf
not sure I got that properly, we would have GDC > sequence features and sibling ICE? or would sequences features be under ICE?
- Melanie
Oh no, the last statement took a large part of my talk away :(
- Robert Hoehndorf
Some questions still about sequence feature as GDC - Are chemical structures also? Or are sequences special because there is evolved machinery for duplicating the features? However - definitely an advance for SO.
- Alan Ruttenberg
@melanie: I believe that current proposal is that there is sequence feature below GDC, but not ICE. But Colin says this is a first step, so the story is not over.
- Alan Ruttenberg
Sequences are special (but not unique) because there is evolved machinery for duplicating the features. Surface geometries are I think GDCs as well because deposition processes constrain where atoms can go.
- Colin Batchelor
Also see Cairns-Smith on the origin of life.
- Colin Batchelor
But in general I would regard chemical structures as qualities and connection tables etc. as GDCs.
- Colin Batchelor
Talk: Using multiple reference ontologies: managing composite annotations: John Gennari
biosimulation models used for teaching, systems biology, patient-specific modeling
- Robert Hoehndorf
models rarely reproducible - need for sharing and reuse
- Robert Hoehndorf
ontologies for physiological modeling: FMA CL for anatomic entities, GO, CheBI, RO, OPB for physical properties, SBO(?) + OPB for physical dependencies, processes (??OBP?)
- Melanie
SBO rocks </disclaimer>
- Melanie
@melanie - wonder if it's SBO we're hearing in the explosions that are shaking the room </disclaimer>
- Alan Ruttenberg
vSPARQL: v = "views" extension of SPARQL
- Melanie
Talk: Metarel: An Ontology to support the inferencing of semantic web relations within biomedical ontologies: Ward Blonde
Meena Kharatmal liked this
metarel capture semantics of relations to allow relational inferencing. Meta-ontology for relations, compatible with RO
- Melanie
metarel is a meta-ontology for relations that exists in OBO, compatible with RO
- Robert Hoehndorf
relational closures (transitivity, reflexivity, compositions) created via SPARUL
- Melanie
ontologies + metarel -> RDF -> using SPARUL to create relations inferences while loading into triplestore, which can then be queried using SPARQL
- Melanie
2 hierarchies: relations + relation type. Classes in the former are instances of the latter.
- Melanie
BioGateway: http://www.semantic-systems-bi...
- Melanie
relational closure x has function y, and y is_a z, then x has_function z
- Melanie
composition x is located in y, and y part of z, then x located in z
- Melanie
Metarel: http://www.semantic-systems-bi...
- Melanie
I like this work. However I worry about the areas in which metarel duplicates expressivity that is already present in OWL, as it represents divergence and poses problems for integrating different resources. E.g. transitivity, subproperty already built in. One possible solution - make sure that both representations are present in the source.
- Alan Ruttenberg
Talk: Providing a realist perspective on the eyeGene Database System: Werner Ceusters
Providing a realist VIEW on the eyeGene Database System would've been a cooler topic for this talk
- Amina Abdulla
eyeGene is a network for eye-disease-causing mutations
- Robert Hoehndorf
eyeGene DB is a repository of genetype and phentype information of patients with eye disease
- Robert Hoehndorf
"A realist view on reality" distinguishs Ontologies, data collections and information models
- Robert Hoehndorf
"A realist view on reality" seems rather circular.
- Robert Hoehndorf
@robert - contrast "a relativist view of reality"
- Alan Ruttenberg
The software demos during lunch were quiet interesting. I was quiet disappointed that they were stopped midway.
Melanie liked this
We need to figure out how to do these better. Problem (at least) - people busy eating somewhere else. Any suggestions?
- Alan Ruttenberg
Having a dedicated time slot for the demos, independent from lunch or break time would help. The demos started late today as there were only a handful of people in the room back from lunch and hence were cut short.
- Amina Abdulla
It would have been nice to start with beer after 8 and have the software demonstrations over beer.
- Robert Hoehndorf
Talk: Towards and ontological representation of resistance: the case of MRSa: Albert Goldfain
Melanie liked this
Based on disease ontology grant
- Robert Hoehndorf
IDO (Infectious Disease Ontology) is a domain ontology based on BFO, part of OBO Foundry
- Robert Hoehndorf
contains Top-level IDO: core ontology of infectious disease domain
- Robert Hoehndorf
IDO extensions: family of reference ontologies for specific diseases and pathogens
- Robert Hoehndorf
Based on dispositional view of disease: disease course exists, bearer of diseasse, part of the bearer (disorder), physical basis of disease
- Robert Hoehndorf
resistence phenomenon: resistance of an individual to a disease, resistance of a tumor to treatment, resistance of a pathogen to a drug, herd immunity of an organism population to a ???, resistance of bacteria to UV, etc
- Robert Hoehndorf
NCI Thesaurus has definition for resistance: uses "resist" in definition, type of resistance unclear: mechanism, function, activity, process? restricted to organism as bearer
- Robert Hoehndorf
desiderata: BFO compatible, positive/active principle: use "lacks" instead of negation; non-proliferation of relations principle: don't add a trivial relation resistant_to, correct granulatiy, pragmatic concerns: IDO/IDO extension terms should mirror scientific interest in resistance types
- Robert Hoehndorf
Resistance as quality vs. disposition: disposition not always manifested, resistance could be quality (sufficiently low susceptibility)
- Robert Hoehndorf
Disposition in BFO 2.0: Dispositions plus Capabilities
- Robert Hoehndorf
Disposition>Capability>Function
- Melanie
But no distinctions between them but their name :) And that capabilities are "good" dispositions and functions "good" capabilities
- Robert Hoehndorf
I can see the capability/function (ie design intent) but I don't know what is a disposition that is not a capability. (wrt to "good" I think there is agreement to not use that as discriminant, and it will be removed - though I may be wrong)
- Melanie
formnalization: 16 triples + 6 inference rules + 5 derived triples
- Robert Hoehndorf
@robert - I'm with you on lack of differentia between capability/disposition
- Alan Ruttenberg
My comments to the discussion about BFO.
s.pdf 49 KB
Melanie liked this
Great, we finally convinced you to talk :)
- Melanie
I think I will just fight windmills there, but somebody has to try :)
- Robert Hoehndorf
I was happy about this presentation :) (speaking as windmill)
- Alan Ruttenberg
Tutorial: From BFO to Information Artifact Ontology, day 1, part 1: Barry Smith
Nico Adams, Peter E Midford, Frank and 2 other people liked this
Ontologies are about integration of data in biology, across different species, across levels of granularity, across different perspectives, within and across disciplines.
- Robert Hoehndorf
Administrative ontologies: locally developed for specific purposes - reusability and compatibility not so important; can be secret, can be bought and sold, may bring entities into existence by the ontology itself.
- Robert Hoehndorf
Scientific ontologies: must go further, science is global and public and open, etc.; science is "seamless" - all parts must interoperate.
- Robert Hoehndorf
Reasons for building scientific ontologies: many ways to build terminologies, multiple terminologies will not solve data silo problems, need to constrain terminologies so that they converge.
- Robert Hoehndorf
What is to serve as constraint for building ontologies? 1 Authority; 2. First in field. 3. Best candidate terminology (what means "best"?). 4. Voting (on what basis?). 5. Reality, as revealed, incrementally, by experimentally-based science.
- Robert Hoehndorf
ontologies are for re-usuability of data using standards, integration of domains
- Meena Kharatmal
ontologies should be representation of Reality. i would opt for 5.
- Meena Kharatmal
Just managed to get on network - I think I will entrust Robert to report, considering his nice notes :)
- Melanie
@Meena: there was some discussion about this, I think it will be discussed further. Personally, I think (5) is wrong, because it gets things upside-down: before you can find natural laws, you already need the ontology; and you can state the same natural law using very different conceptualizations. The best example is probably geometry, for which complete axiom systems were developed based on many different ontologies.
- Robert Hoehndorf
BFO 1.0 in 2004, based on Aristotelian ontology. First major revision in 2008, adding generically dependent continuants. BFO 2.0 coming soon: incorporate top-level relation from the OBO RO into BFO 1.1, and ensure that all relations internal to BFO (dependence) are included.
- Robert Hoehndorf
New Relation Ontology coming soon, too; about twice the size of original one.
- Robert Hoehndorf
Kinds of relation: universal-universal, individual-universal, individual-individual.
- Robert Hoehndorf
Ontological realism: get real ontology right first and then investigate ways in which this real ontology can be translated into computer-usable form later.
- Robert Hoehndorf
Method of ontological realism: find out what the world is like by doing science, talking to other scientists and working continuously with them to ensure that you don't go wrong; create ontologies adequate to this world, not to some simplified model; build representations of entities in the world, not of concepts
- Robert Hoehndorf
ontologies must be able to change if science changes
- Melanie
The mechanism to develop "stuff" in a language independent manner in computer science is to use UML and then realise in concrete forms, Java object, XML, etc. The ontology has to be represented in something formal, it cant just be a story...
- Frank
main distinction between universal and instance
- Robert Hoehndorf
science texts are about universals, diaries are about instances
- Melanie
avoid word concept :)
- Melanie
why? concepts are good
- Frank
ontologies are representation of universals in reality
- Meena Kharatmal
BFO wants to be compatible with higher-order universals, but does not use it at the current moment.
- Robert Hoehndorf
Each term in an ontology represents exactly one universal (and should be referred to using singular nouns.
- Robert Hoehndorf
Three levels: entities in reality, both instances and universals; cognitive representations of this reality; publicly accessible concretizations of these cognitive representations
- Robert Hoehndorf
ontolgoy development starts with level 2 = cognitive representations
- Robert Hoehndorf
and can result in level 3 - concretizations of cognitive representations.
- Meena Kharatmal
extension of universal A is the collection of all particulars A: a class is such a collection
- Melanie
defined classes (eg brother of elvis fan) doesn't correpond to any universal
- Melanie
a scientific ontology is a representational artifact which is intended to represent universals and some defined classes.
- Robert Hoehndorf
Both DOLCE and BFO are heavily influenced by Aristotle (although I am not sure if Claudio Masolo or Nicola would agree with that on the DOLCE part).
- Robert Hoehndorf
BFO is a true upper level ontology, no interference with domain ontologies and issues of cognition, no fiction, "small subset of DOLCE but with a clearer treatment of instances, universals, relations and qualities, time"
- Robert Hoehndorf
On a personal note: the last sentence is rather funny, considering that BFO has no axioms for relations, time, qualities, etc. while DOLCE has a very elabnorate axiom system for these...
- Robert Hoehndorf
time problem: distinction between what exists and what occurs: I exist, this arm movement occurs
- Melanie
process entities = occurrents / continuants = things that exist
- Melanie
parthood depends on time: eg molecule can be part of tumor at one point and not an other -> continuants can gain and loose parts and preserver their identity, not true for occurrents
- Melanie
Occurrents are dependent on a continuant
- Robert Hoehndorf
sameas.org is some project about keeping track of identity (???); but apparently it is bad because they get things wrong about the continuant/occurrent distinction
- Robert Hoehndorf
that is a very big claim that "BFO is a true upper level ontology", maybe is should be written that BFO is aiming to be a true upper ontology. If it is, it would not be putting out a new version
- Frank
see current discussion on public-lod about the sameAs website and the ramalteon example - http://markmail.org/message...
- Melanie
Slides are at http://icbo.buffalo.edu/present...
- Robert Hoehndorf
Continuants divided into independent and dependent
- Robert Hoehndorf
One-place dependent continuants and relational dependent continuants.
- Robert Hoehndorf
Dependence relations between processes and substances; also one-place (getting warmer) and relational.
- Robert Hoehndorf
Three dichotomies: instance vs. universal, continuant vs. occurrent, dependent vs. independent
- Robert Hoehndorf
Every functioning (process) is dependent on some function (dependent continuant)
- Robert Hoehndorf
Universal-Universal relations are always All-Some Relations (R(C,D) <-> C subclassof (some R D)
- Robert Hoehndorf
There are some some-some relations. They should not be included in an ontology, because they do not support reasoning. Rather, relevant instance-level relations should be included, as well as probabilistic relations at the type level.
- Robert Hoehndorf
Short interruption about absent nipples and possible fevers.
- Robert Hoehndorf
Melanie knows I have a whole car full of absent nipples - anybody want one?
- Frank
Relations between occurrents and continuants via relations: dependence, participation, realization.
- Robert Hoehndorf
and that is *why* I didn't post about that example :)
- Melanie
Realization: execution of plan, expression of function, exercise role,...
- Robert Hoehndorf
Realizable dependent entitites: plan, function, role, disposition, algorithm,...
- Robert Hoehndorf
A role is an individual, which exists only while the role is being exercised.
- Robert Hoehndorf
A role is temporary, an entity can loose the role when the process ends
- Frank
What is a role: realizable entity, which exists because the bearer is in some special physical social or institutional set of circumstances in which the bearer does not have to be, and is not such that, if it ceases to exists, then the physical make-up of the bearer is thereby changed.
- Robert Hoehndorf
student_role instance starts existing at 9.00 am and end up at 12.30; there is being a student_role in this class, and a student_role in general
- Melanie
Disposition (internally grounded realizable entity): a realizable entity which if it ceases to exist, then its bearer is physically changed, and whose realization occurs when this bearer is in some special physical circumstances, in virtue of the bearer's physical make-up.
- Robert Hoehndorf
examples: fragility to break, solubility when placed in liquid..
- Melanie
Dispositions cannot be lost or gained without a physical change in the disposition's bearer.
- Robert Hoehndorf
Capability (new realizable): a disposition that exists in virtue of the bearer's physical make-up, and enables the entity in which it inheres to particpate in events of a certain kind.
- Robert Hoehndorf
yay - speaking french is officially barry-approved a good disposition :)
- Melanie
function = capability that exist due to design (evolution, human...)
- Melanie
The capability definition does not add anything to dispositions, IMHO: the first part is just a consequence of the "physical make-up" part of the disposition def, the second is trivially true without further explanation.
- Robert Hoehndorf
Barry: organisms don't have functions.
- Robert Hoehndorf
Parts of organisms have functions.
- Robert Hoehndorf
There such a thing as a "canonical life plan".
- Robert Hoehndorf
An entity has a biological function iff it is part of an organism and has a disposition to act reliably in such a way as to contribute to the organism's realization of the canonical life plan for an organism of that type.
- Robert Hoehndorf
What is a disease? functions are "good" dispositions, relevant to the realization ofthe canonical life plan; diseases are "counterpart bad dispositions"
- Robert Hoehndorf
Disposition divided into: Function and Disease
- Robert Hoehndorf
I agree with Alan and don't like that good/bad distinction - I am not sure how to define those, and in my opinion they are totally subjective and context-dependent
- Melanie
That is only one side of the story - for example, diseases are good for the parasite - its how they survivie and reproduce. IMO diseases are a collection of processes - not a disposition
- Frank
I don't even like "canonical life plans". Where are the instances?
- Robert Hoehndorf
I think Barry has been reading to many celebrity life-style magazines to come up with a "canonical life plane"
- Frank
@Frank: I think they want to claim that diseases can be there even when they are not manifest. So there are processes which are disease-manifestestions, while the disease is the disposition for these manifestations.
- Robert Hoehndorf
Information objects: pdfg file, poems, symbols, sequence, molecular structure, etc.
- Robert Hoehndorf
the disease course is the collection of processes
- Melanie
Information objects are generically dependent continuants.
- Robert Hoehndorf
well, diseases are a collection of observed processes, a specific set of observed process can be collectively known as a disease. A dissease course is also a process - the progression of the observed processes that make up the collective disease - I dont believe dispositions are helpful in trying to define diseases
- Frank
GDCs are divided into information objects and sequences.
- Robert Hoehndorf
i would like to think as: disease is a "state" of body, as "healthy" is a state of body
- Meena Kharatmal
@Meena: but then, what is a state? You mean DOLCE's statives?
- Robert Hoehndorf
don't like either distinction between information entities and sequences. IMO, sequences, structure etc are information entities.
- Melanie
@Melanie: I agree; I am waiting for the distinctive properties to come up in one of the next slides.
- Robert Hoehndorf
I'm waiting for the IAO talk tomorrow to ask about differentiae :)
- Melanie
Information entities exist in a way which makes them dependent on provenance and on proccessors, in a way in which types are not.
- Robert Hoehndorf
I think GDC and SDC are the result of over-engineering, the current distinction is blurry and I dont think its helpful dependent continuant is sufficient.
- Frank
If I am unlucky I will have to restructure my talk about sequences after listening to the tutorials today and tomorrow.
- Robert Hoehndorf
Human is not a universal, but a GDC.
- Robert Hoehndorf
Note: In BFO, every universal is generically dependent on its instances.
- Robert Hoehndorf
@Robert: states represented as properties of objects
- Meena Kharatmal
homo sapiens is the class that exemplifies the concretization of the GDC
- Melanie
@Meena: aaaah, states of affairs; I love states of affairs, especially negative ones :)
- Robert Hoehndorf
@meena - states/properties relation is wrong. This would type properties of objects as "representations", which they are not. They are the things that representations represent
- Alan Ruttenberg
am not sure having the GDC brings anything - if I understood correctly, the GDC is the genome quality that makes the human be a human - seems a bit...over-engineered :)
- Melanie
@Melanie: I wonder which universal could not be rewritten as the class of all things exemplifying a GDC.
- Robert Hoehndorf
@melanie - its a dependency counting thing again. On what things does the genome quality depend
- Alan Ruttenberg
when does it go out of existence?
- Alan Ruttenberg
let me put forth the following: disintegration a process of an object nuclear envelope, prior state of nuclear envelope is continuous and post state of nuclear envelope is fragmented as a result of the process of disintegration.
- Meena Kharatmal
@Meena 1-5 are an artificial distinction. What is the experimental evidence for numbers? The are still useful. Besides, the idea that we should get "reality" right first, then worry about computational applications is non-sensical; it's like suggesting we should get physics right first, then worry about a mathematical representation.
- Phil Lord
Is there really a distinction to be made between qualities and dispositions?
Peter E Midford and Allyson Lister liked this
what are the consequences loosing the distinction? Until now, I haven't seen any example of gain by making it.
- Melanie
Analysis by dependency counting? Qualities depend on bearer. Dispositions depend on bearer and realizing process.
- Alan Ruttenberg
Even so, that justifies that you can make the distinction (realized or not in process), but doesn't tell me what is the benefit of making it? In which context may it be important to know "that is a quality and not a disposition", and vice versa?
- Melanie
Frank, tend to agree. If a disposition necessarily requires a process, while a quality doesn't, then colour is a disposition, or rather a perception of a disposition (which is reflectance). Mass or height don't need a process though.
- Phil Lord
@Phil, Is gravity a process? :) - ok, yes mass has nothing to do with gravity, hight probably does, although you could reword it to "dimensions" to have less connotations with "growing"
- Frank
that last comment was not meant to read that height has anything to do with gravity, rather it has something to do with a process...
- Frank
@Frank mass is measurable with a process (graviational attraction, or acceleration) but conceptually seems not to depend on this. Of course, I realise that the physics are very thin here. Anything with mass will always be involved in graviational attraction. I'm not sure that the distinction between the two is justifiable from physics. I think Melanies original questions is the most important one. Is the conceptual distinction between the two useful in the social context of model building in science?
- Phil Lord
Frank liked this
Classical mereology - 2 kinds of entities that can be quantified over (== objects) and collections of (needing for summing together collections of objects)
- Melanie
1 mereological primitive: P, binary predicate, Pxy == x is part of y
- Melanie
Definitions PPxy: proper part: object has other parts: x is part of y and x isn't identical to y overlaps: some object is part of both x and y, they share a part
- Melanie
(theorem: if x is part of y, x and y overlap. Eg if foot part of body, foot and body overlap) DSxy: x and y are discrete, x and y do not overlap SUM(x, A): first argument is individual, second argument is a collection of objects piece of chalk is sum of all chalk molecules in, every molecule is part of this piece of chalk, and every other part overlaps at least one of the molecule (in fact several) in this piece of chalk
- Melanie
5 axioms: 1. reflexive: every object is part of itself (otherwise we use proper part) 2. transitive 3. antisymmetric: if x part of y and y is part of x, x and y are identical 4. Strong supplementation principle: if x is not part of y, then x has some part that is discrete from y 5. Universal fusion principle: every non-empty collectio of object has a sum: there is some object that is made up of piece of chalk and piece of empire state building
- Melanie
Some theorems: T1. if everything that overlaps x also overlaps y, then x is part of y T2. if x and y overlap the same thing, x and y are identical T3. every collection of individuals has at most one sum: : if x is the sum of A, and y is the sum of A, then x and y are identical
- Melanie
model for classical mereology: - parthood is interpreted as subset relation - proper parthood would be the proper subset relation - overlap would be set of Si, Sj (which are subset of S) where Si intersection Sj is not empty (2 subsets overlap if they have a non empty intersection) - discrete: relation that holds between subsets of S that have non overlapping parts - summation: union of all subsets in our domain
- Melanie
weaker mereology why do we need a weaker mereology: some non intuitive axioms, e.g. - A5: there is some object which is the sum of my left hand and the empire state building, and that seems counter intuitive to some people - if x sum of A and y is the sum of A then x and y are identical: some people think that is too strong: idea is that we can have two distinct objects composed of same collection of same molecules
- Melanie
example: play-doh, molded in a cup. this clay has been sitting home for over a year, removed it this morning and took it out from her backpack. some people would say there is an other object here than a cup, that was not at her house this morning, and that a lump of clay has been pulled out of backpack and not a cup. it looks like the cup has to be distinct from the clay, the cup came to existence only moments ago.
- Melanie
temporal mereology (disclaimer - I may be mereology saturated by now ;) )
- Melanie
Curious about how part of different aspects of things interact. E.g. part of on object, relation to part of on the regions that contain the objects. Or part of for information entity, compared to part of in the concretizations.
- Alan Ruttenberg
temporal version of classical mereology entities: objects (w,x,y,z), collections of objects (A,B,C) and time (s, t) one mereological primitvie: ternary predicate, takes 2 objects and time as argument: Pxyt: object x is part of object y at time t
- Melanie
PPxyt: x is a proper part of y at t: x is part of y t time t and y is not part of x at t Oxyt: x and y overlap at t DSxyt: x and y are discrete at t Ext=: Pxxt (x exists at time t)
- Melanie
@alan: part of information entities are really tough, because the same information entities can be part of another one multiple times; and suddenly, you don't have supplementation anymore, and, arguably, no more part-of relation.
- Robert Hoehndorf
mixture example: lemonade - whenever a portion of lemonade is there, all its molecules have to be there and their sum is the portion of lemonade, but at any other time the lemonade molecules are scattered in other places When lemonade is there, it has to be made up of just these components: we wouldn't have same portion of lemonade if we were having different components, it would be a different lemonade
- Melanie
I agree, see my very old video http://www.bioscreencast.com/bsc_mov...
- Frank
mereotopologies Cxy: x is connected to y. There is no need for physical attachment, but x is zero distance to y (for a temporal theory we would use a ternary predicate Cxyt: x is connected to y at time t)
- Melanie
Axioms: AC1: connection is reflexive, everything is connected to itself AC2: symmetric, if x connected to y, y is connected to x AC3: if x part of y, then everything that is connected to x is connected to y
- Melanie
the last axioms, AC3, does not seem to be very intuitive: if I have a square y and take a circle in the middle of the square x, then there are things that are connected to x (the remaining parts of y), but it seems weird to say that these parts of y are also connect to y.
- Robert Hoehndorf
@robert: somebody mentioned the same, apparently we are talking about "internal connection", and by definition if you are connected to one, you are connected to the other.
- Melanie
Containment relations addition of vocabulary for material: we add immaterial objects, holes, cavities.... we add a unary region function r which maps an object or region to the region it is located in. r(x) is interpreted as the spatial region at which x is exactly located
- Melanie
AC1: if x is a propert part of y, then x's region is proper part of y's region AC2: x's spatial region is its own spatial region Region containment: RCONxy =: Pr(x)r(y) x is region-contained in y means x's region is part of y's region different of part of for example; my heart is region contained in my middle mediastinal space my larynx is region contained in my neck While the larynx is part of my neck, the heart is not part of the mediastinal space
- Melanie
Convex hull: the convex hull of an object or region is the smallest convex region in which x is region-contained. ch(x) is x's convex hull (convex: between 2 points of the set you can draw a line that stays in your set, eg circles are convex))
- Melanie
Surrounding relation: x is surrounded by y means that x's region is part of y's convex hull while x's region are being discrete from y's regio (x is not located where y is located) example: my pleural space is surrounded by my pleural membrane. A bolus of food is surrounded by the wall of my stomach.
- Melanie
Partial containment: PCONxy =: Or(x)ch(y) x is partially contained in y if x's regions overlap y's convex hull example: my oesophagus is partially contained in my thoracic cavity. My tooth is partailly contained in its socket.
- Melanie
those relations have different properties: RCON is transitive, SUR and PCON are not. example: - my heart is RCON in my mediastinal space, and my mediastinal space is RCON in my thoracic cavity, my heart is RCON in my thoracic cavity - a filling is PCON in my tooth, and my tooth is PCON in its socket, but the filing is not PCON in the socket.
- Melanie
- if my heart is RCON in my mediastinal spac, then any part of my heart is RCON in my mediastinal space - my tooth is PCON in its socket even though some of its parts are not PCON in the socket
- Melanie
X is fragile if and only if whenever X is placed in the right circumstances, it will always cause a process of a certain kind; X participates in this process (in a certain role) and is broken at the end. "Being placed in the right circumstances" is a description of situation types together with a role X must play within these situations.
Well, this will probably not be the best definition ever...
- Robert Hoehndorf
Alternative: X is fragile if some entity similar to X has broken before.
- Robert Hoehndorf
Alternative: The probability of breakage given a stimulus on X is increased.
- Robert Hoehndorf
First - scope of fragile. Are flowers fragile? Is paper fragile? Can a gas be fragile?
- Alan Ruttenberg
Maybe: x is fragile iff there is a possible situation type with a role that x can play, such that whenever x is placed in a situation of this type playing the specified role, a breaking process is caused (through laws of nature).
- Robert Hoehndorf
Alternative: x possesses certain properties and the laws of nature are as they are.
- Robert Hoehndorf
Simple conditional analysis: something x is disposed at time t to give response r to stimulus s, iff, if x were to undergo s at t, x would r.
- Robert Hoehndorf
@alan: good question; I guess, it depends what the outcome of a manifestation of the "fragile" disposition would be; my answer would be that flowers can break, paper can break, gas can break (you can freeze it and then break it); but I can easily see how you would answer that differently.
- Robert Hoehndorf
Reformed conditional analysis of dispositions (based on D. Lewis' paper about finish dispositions): Something x is disposed at time t to r to stimulus s, iff, for some intinsic property b that x has at t and for some time t' after t, if x were to undergo s at t, and retain b until t', s and x's having b would be an x-complete cause of x's giving r.
- Robert Hoehndorf
SIG: Bio-Ontologies: Contributions to the formal ontology of functions and dispositions: An application of non-monotonic reasoning, Robert Hoehndorf et al.
the function of my head is to ache in the morning
- Phil Lord
Larry Wright says that the function of X is Z and this means: X is there because it does Z; Z is a consequence (or result) of X's being there. The heart is there because it pumps blood, and pumping blood is a consequence of the heart being there. But this doesn't work for "the heart makes pumping noises", as the heart isn't there to make pumping noises. Therefore you need some refinements.
- Allyson Lister
although the heart is there because it grew; it don't pump blood when you are dead
- Phil Lord
What does Larry say "because" means ;-)
- Alan Ruttenberg
@Alan: For him, "because" is a causal relation. So, hearts pump blood (now), and hearts' pumping blood (in the past) causes hearts to exist now.
- Robert Hoehndorf
Does he give conditions for when causation exists?
- Alan Ruttenberg
that be-"cause" is a "caus"al relation doesn't add anything
- Alan Ruttenberg
Larry Wright does not say anything more about causation, he uses it as a primitive relation. Although we seem to have good intuitions about causation, in philosophy, there are probably more theories of causation than there are philosophers. So I agree, this remains a weak point in any definition of function that uses "causation".
- Robert Hoehndorf
Life sciences on the Semantic Web: the Neurocommons and beyond. - http://www.citeulike.org/user...
Frank, Berci Mesko, MD, Deepak Singh and Pierre Lindenbaum liked this
And the reason a science commons paper is not open access is...........?
- Frank
@Frank -- none of the authors appear to be affiliated with SC. Agree it's weird they wouldn't choose an OA journal though, if they're such fans as to be writing about NeuroCommons.
- Bill Hooker
I have the PDF, so PM me if you would like a copy
- Graham Steel
Two of the authors are associated with Science Commons, one of them being me. Let me apologize for the open access issue. There were circumstances. We'll try to remedy the situation, but in the mean time I'm happy to supply a reprint (PDF) to anyone who requests on. Skype me at alanruttenberg or send me email at alanruttenberg@gmail.com
- Alan Ruttenberg
@Alan, yeah! first post on FriendFeed :)
- Frank
Thanks, Alan.
- Graham Steel
Sweet! I should have looked harder for the SC connection, obviously.
- Bill Hooker
You can access the full text here: http://tinyurl.com/ckhmhp
- Alan Ruttenberg
excellent, thanks Alan
- Frank
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