https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=AlanrNCBO Wiki - User contributions [en]2026-06-05T14:43:29ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=Alzforum_/_Protein_Ontology_Kick-Off_Meeting&diff=10977Alzforum / Protein Ontology Kick-Off Meeting2011-07-25T05:45:27Z<p>Alanr: /* Intending Participants */</p>
<hr />
<div>'''Date and Venue'''<br />
<br />
October 4-5, Buffalo, NY<br />
<br />
==Goals of the meeting==<br />
<br />
The goal of this meeting is to initiate a project that is designed to lead to the creation of a protein information resource that will address the needs of Alzheimers Disease (AD) researchers in a maximally effective way. <br />
<br />
The project forms part of the NIGMS-funded Protein Ontology initiative. Topics to be addressed at the meeting will include<br />
<br />
'''Protein Variants'''<br />
How can we most effectively represent information pertaining to the variants associated with AD and to the relations between them; for example, what level of specificity of descriptions of variants would best address the requirements of AD researchers? In the case of APP, for example, what are the genetic variants of relevance to APP? How should the Protein Ontology deal with such variants in order to assist researchers.<br />
<br />
'''Aggregates of proteins / Protein complexes'''<br />
What are the different kinds of aggregates and complexes relevant to AD, how do AD researchers treat them? <br />
<br />
We envisage two case studies in the course of the meeting, both of which will be designed to serve as guidance for Protein Ontology developers in the initial phases of the project:<br />
<br />
1. Protein case study: Perform a detailed review of one class of proteins important to AD research, chosen to be part of the research agenda of at least one of the AD scientists, to bring all participants up to the same level of understanding about what os known. Issues to be addressed will include: <br />
:: importance of recording non-protein constituents <br />
:: multimerism<br />
:: relations to disease hypotheses <br />
:: kinds of evidence<br />
:: research plan<br />
:: protein knowledge queries that would aid the AD researchers<br />
:: protein knowledge queries the AD researchers think their colleagues ought to be able to do that would retrieve their own results<br />
<br />
2. Protein complex case study: In addition to the issues addressed above as these arise for protein complexes, this case study will address in addition: criteria for being a complex - what amount of stability is necessary, component stoichiometry and structure, modifications/changes to complexes and associated functional changes.<br />
<br />
==Very Tentative Schedule==<br />
<br />
'''Tuesday, October 4'''<br />
<br />
9:30am<br />
<br />
*Introduction to the project; introduction of project personnel<br />
*Introduction to the AD research problems to be addressed<br />
*Introduction to ontology for scientists<br />
<br />
10:30am Break<br />
<br />
11:00am<br />
<br />
*Short tutorial on the Protein Ontology and associated web tools (including feedback) <br />
*Review of proteomics information tools, resources used by AD researchers, unmet needs<br />
<br />
12:30pm Lunch<br />
<br />
1:30pm Session on variants, complexes, aggregates<br />
<br />
6:00pm Dinner<br />
<br />
'''Wednesday, October 5'''<br />
<br />
9:00am Case Studies <br />
<br />
12:30pm Lunch<br />
<br />
1:30pm Case Studies<br />
<br />
2:30pm Project planning<br />
<br />
3:30pm Main meeting ends<br />
<br />
Technical session for selected participants during rest of day.<br />
<br />
==Intending Participants==<br />
*Cecilia Arighi (University of Delaware)<br />
*Peter d'Eustachio (Reactome, New York)<br />
*Alex Diehl (University at Buffalo)<br />
*Darren Natale (Georgetown University Medical Center, Washington DC)<br />
*Alan Ruttenberg (University at Buffalo)<br />
*Barry Smith (University at Buffalo)<br />
*Kinga Szigati (University at Buffalo) <br />
*Michael Wolfe (Harvard Medical School, Boston)<br />
*Cathy Wu (University of Delaware)<br />
*Elizabeth Wu (Alzforum, Boston)</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=Alzforum_/_Protein_Ontology_Kick-Off_Meeting&diff=10976Alzforum / Protein Ontology Kick-Off Meeting2011-07-25T05:39:56Z<p>Alanr: /* Very Tentative Schedule */</p>
<hr />
<div>'''Date and Venue'''<br />
<br />
October 4-5, Buffalo, NY<br />
<br />
==Goals of the meeting==<br />
<br />
The goal of this meeting is to initiate a project that is designed to lead to the creation of a protein information resource that will address the needs of Alzheimers Disease (AD) researchers in a maximally effective way. <br />
<br />
The project forms part of the NIGMS-funded Protein Ontology initiative. Topics to be addressed at the meeting will include<br />
<br />
'''Protein Variants'''<br />
How can we most effectively represent information pertaining to the variants associated with AD and to the relations between them; for example, what level of specificity of descriptions of variants would best address the requirements of AD researchers? In the case of APP, for example, what are the genetic variants of relevance to APP? How should the Protein Ontology deal with such variants in order to assist researchers.<br />
<br />
'''Aggregates of proteins / Protein complexes'''<br />
What are the different kinds of aggregates and complexes relevant to AD, how do AD researchers treat them? <br />
<br />
We envisage two case studies in the course of the meeting, both of which will be designed to serve as guidance for Protein Ontology developers in the initial phases of the project:<br />
<br />
1. Protein case study: Perform a detailed review of one class of proteins important to AD research, chosen to be part of the research agenda of at least one of the AD scientists, to bring all participants up to the same level of understanding about what os known. Issues to be addressed will include: <br />
:: importance of recording non-protein constituents <br />
:: multimerism<br />
:: relations to disease hypotheses <br />
:: kinds of evidence<br />
:: research plan<br />
:: protein knowledge queries that would aid the AD researchers<br />
:: protein knowledge queries the AD researchers think their colleagues ought to be able to do that would retrieve their own results<br />
<br />
2. Protein complex case study: In addition to the issues addressed above as these arise for protein complexes, this case study will address in addition: criteria for being a complex - what amount of stability is necessary, component stoichiometry and structure, modifications/changes to complexes and associated functional changes.<br />
<br />
==Very Tentative Schedule==<br />
<br />
'''Tuesday, October 4'''<br />
<br />
9:30am<br />
<br />
*Introduction to the project; introduction of project personnel<br />
*Introduction to the AD research problems to be addressed<br />
*Introduction to ontology for scientists<br />
<br />
10:30am Break<br />
<br />
11:00am<br />
<br />
*Short tutorial on the Protein Ontology and associated web tools (including feedback) <br />
*Review of proteomics information tools, resources used by AD researchers, unmet needs<br />
<br />
12:30pm Lunch<br />
<br />
1:30pm Session on variants, complexes, aggregates<br />
<br />
6:00pm Dinner<br />
<br />
'''Wednesday, October 5'''<br />
<br />
9:00am Case Studies <br />
<br />
12:30pm Lunch<br />
<br />
1:30pm Case Studies<br />
<br />
2:30pm Project planning<br />
<br />
3:30pm Main meeting ends<br />
<br />
Technical session for selected participants during rest of day.<br />
<br />
==Intending Participants==<br />
*Cecilia Arighi (Delaware)<br />
*Peter d'Eustachio (New York)<br />
*Alex Diehl (Buffalo)<br />
*Darren Natale (Washington)<br />
*Alan Ruttenberg (Buffalo)<br />
*Kinga Szigati (Buffalo) <br />
*Barry Smith (Buffalo)<br />
*Cathy Wu (Delaware)<br />
*Elizabeth Wu (Boston)</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=Alzforum_/_Protein_Ontology_Kick-Off_Meeting&diff=10975Alzforum / Protein Ontology Kick-Off Meeting2011-07-25T05:39:41Z<p>Alanr: /* Very Tentative Schedule */ - some minor mods</p>
<hr />
<div>'''Date and Venue'''<br />
<br />
October 4-5, Buffalo, NY<br />
<br />
==Goals of the meeting==<br />
<br />
The goal of this meeting is to initiate a project that is designed to lead to the creation of a protein information resource that will address the needs of Alzheimers Disease (AD) researchers in a maximally effective way. <br />
<br />
The project forms part of the NIGMS-funded Protein Ontology initiative. Topics to be addressed at the meeting will include<br />
<br />
'''Protein Variants'''<br />
How can we most effectively represent information pertaining to the variants associated with AD and to the relations between them; for example, what level of specificity of descriptions of variants would best address the requirements of AD researchers? In the case of APP, for example, what are the genetic variants of relevance to APP? How should the Protein Ontology deal with such variants in order to assist researchers.<br />
<br />
'''Aggregates of proteins / Protein complexes'''<br />
What are the different kinds of aggregates and complexes relevant to AD, how do AD researchers treat them? <br />
<br />
We envisage two case studies in the course of the meeting, both of which will be designed to serve as guidance for Protein Ontology developers in the initial phases of the project:<br />
<br />
1. Protein case study: Perform a detailed review of one class of proteins important to AD research, chosen to be part of the research agenda of at least one of the AD scientists, to bring all participants up to the same level of understanding about what os known. Issues to be addressed will include: <br />
:: importance of recording non-protein constituents <br />
:: multimerism<br />
:: relations to disease hypotheses <br />
:: kinds of evidence<br />
:: research plan<br />
:: protein knowledge queries that would aid the AD researchers<br />
:: protein knowledge queries the AD researchers think their colleagues ought to be able to do that would retrieve their own results<br />
<br />
2. Protein complex case study: In addition to the issues addressed above as these arise for protein complexes, this case study will address in addition: criteria for being a complex - what amount of stability is necessary, component stoichiometry and structure, modifications/changes to complexes and associated functional changes.<br />
<br />
==Very Tentative Schedule==<br />
<br />
'''Tuesday, October 4'''<br />
<br />
9:30am<br />
<br />
*Introduction to the project; introduction of project personnel<br />
*Introduction to the AD research problems to be addressed<br />
*Introduction to ontology for scientists<br />
<br />
10:30am Break<br />
<br />
11:00am<br />
<br />
*Short tutorial on the Protein Ontology and associated web tools (including feedback) <br />
*Review of proteomics information tools, resources used by AD researchers, unmet needs<br />
<br />
12:30pm Lunch<br />
<br />
1:30pm Session on variants, complexes, aggregates<br />
<br />
6:00pm Dinner<br />
<br />
'''Tuesday, October 4'''<br />
<br />
9:00am Case Studies <br />
<br />
12:30pm Lunch<br />
<br />
1:30pm Case Studies<br />
<br />
2:30pm Project planning<br />
<br />
3:30pm Main meeting ends<br />
<br />
Technical session for selected participants during rest of day.<br />
<br />
==Intending Participants==<br />
*Cecilia Arighi (Delaware)<br />
*Peter d'Eustachio (New York)<br />
*Alex Diehl (Buffalo)<br />
*Darren Natale (Washington)<br />
*Alan Ruttenberg (Buffalo)<br />
*Kinga Szigati (Buffalo) <br />
*Barry Smith (Buffalo)<br />
*Cathy Wu (Delaware)<br />
*Elizabeth Wu (Boston)</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=9760RO:Main Page2010-03-01T17:52:27Z<p>Alanr: /* Errata in Relations paper */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
An RO expert meeting took place in May, 2008. See [[OntologyRelations]] for notes and presentations.<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
Mike And Chris' Relation Ontology Proposed (MACROP), a list targets relations is [[MACROP]]<br />
<br />
==Proposal regarding defined classes==<br />
<br />
We take 'type' as primitive; types are children of BFO categories, which are themselves types. In the definitions that follow we ignore the factor of time, which should however be made explicit according to the practices established in RO.<br />
<br />
extension =def. the class [collection, totality, set] of all instances of a type<br />
<br />
defined class =def. a class all of whose members instantiate the same type T, that is (1) not itself the extension of any type, (2) defined by means of a statement of necessary and sufficient conditions of the form 'A ... is a T which ...'.<br />
<br />
Example: all people holding violins in the La Scala Opera House at a certain time.<br />
<br />
composite class =def. a class all of whose members instantiate one or other of a number of types, T1, ... Tn, that is (1) not itself the extension of any type, (2) defined by means of a disjunction of statements giving necessary and sufficient conditions of the form 'A ... is either a T1 which ... or a Tn which ...'<br />
<br />
Example: all people or bacteria in the La Scala Opera House at a certain time; the pattern '...' exemplified by graphical instances and by morse code beeps.<br />
<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
On the logic of instance-level relations see also Bittner's paper [http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner_AO_07-60_printed.pdf here].<br />
<br />
==Proposed new type-level relations (posted by Melanie Courtot) ==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on <br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
Some of those are described in the [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo RO proposed] file.<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
:name: regulates<br />
:def: "A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process" []<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
:name: positively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
:name: negatively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
:ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_relations_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page <br />
:[https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]<br />
<br />
<br />
==Need for Specific Role Relations (BS)==<br />
<br />
x has a role => x is assigned the role e.g. in the protocol<br />
x realizes the role => x has the role<br />
x plays the role => x performs those actions which someone who has the role would perform if they were realizing it<br />
<br />
Someone who has a role can also play it<br />
But so also can someone who does not have the role, e.g. the doctor takes on the nurse role because the nurse is off sick.<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Note, the term 'homology' has had many uses. This is an attempt to formally define 'cladistic homology'. One possible informal way to define this: "similarity due to unbroken descent from a common ancestor" ('Developmental Plasticity and Evolution', Mary West-Eberhard (2003))<br />
<br />
<br />
<br />
x1 '''derived_by_direct_descent_from''' x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism<br />
<br />
- x1 is an anatomical structure<br />
<br />
- x1 '''part_of''' y1<br />
<br />
- y2 is an organism<br />
<br />
- x2 is an anatomical structure<br />
<br />
- x2 '''part_of''' y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of y2. *(see notes below)<br />
<br />
'''derived_by_descent_from''' is the instance level relation which is the transitive closure over '''derived_by_direct_descent_from'''<br />
<br />
From this we can define a type level relation:<br />
<br />
A in B ''derived_by_descent_from'' C in D :<br />
<br />
For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)<br />
<br />
a '''part_of''' b<br />
<br />
a '''derived_by_descent_from''' c<br />
<br />
c '''part_of''' d<br />
<br />
(Note – B must be a subclade of the clade genealogically descended from D)<br />
<br />
A1 in B1 ''homologous_to A2'' in B2<br />
<br />
iff<br />
<br />
exists A3, B3:<br />
<br />
A1 in B1 ''derived_by_descent_from'' A3 in B3<br />
<br />
&<br />
<br />
A2 in B2 ''derived_by_descent_from'' A3 in B3<br />
<br />
(Note B1 and B2 must both be subclades of the clade descending (in the genealogical sense) from D)<br />
<br />
[* This clause still needs some work]<br />
<br />
[* On the Phenoscape project list, Jim Balhoff added the following critique of this:<br />
<br />
Something that jumps out at me in the definition of derived_by_direct_descent_from:<br />
<br />
I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]<br />
<br />
[* DS: comment - I agree that reference to genetic sequence is (probably) unnecessary. Anyway, it is clear that the current formulation doesn't work: The morphology of my leg is determined by a partial copy of the genetic sequence that determined morphology of my father's arm. One possible alternative, deliberately ignoring genetics: Of all the anatomical structures in y2, x2 is the most morphologically similar to x1.<br />
]<br />
<br />
Note: Do we need to include time (exists & existed)? <br />
<br />
FN – just to be on the safe side we can include time – it's not obviously useful but it could block some objections and won't affect the logic.<br />
<br />
=== relation to what is in RO proposed ===<br />
<br />
Note that there are a number of synonyms for derived_by_descent_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language<br />
<br />
== Measurements ==<br />
<br />
At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation<br />
called is_measurement_of to relate a measurement to some entity. (I<br />
can't remember if these were the exact names we used).<br />
is_measurement_of is subpropertyOf is_about<br />
<br />
In the following we are discussing instance level relationships.<br />
<br />
* measurement_datum:<br />
** has_value:<br />
** in_units:<br />
** of_dimension:<br />
<br />
m1 type measurement:<br />
<br />
* m1 has_value 30^^xsd:float<br />
* m1 in_units_of degree_celsius (UO:0000027)<br />
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)<br />
<br />
(Unresolved: latter two are classes. I guess that means that<br />
in_units_of and of_dimension are annotation properties, which is a<br />
shame. Either that or degree_celsius and temperature_dimension are<br />
instances of some sort. Barry?)<br />
<br />
* room1 type site<br />
* room1 has_quality t1<br />
* t1 instance_of temperature (PATO:0000146)<br />
<br />
* m1 is_measurement_of t1<br />
<br />
It was left open exactly how to represent uncertainty in the<br />
measurement, but this was thought to be perhaps something associated<br />
with the instrument or with a collection of measurements, rather than<br />
what was associated with the individual measurement.<br />
<br />
Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z<br />
<br />
== Realization_of and Associated Relations == <br />
<br />
For OBI purposes there is a need for an instance-level relation between a plan (for instance a protocol) and the occurrent which realizes this plan.<br />
<br />
In its terms we might define, for example,<br />
<br />
x deviation_from y<br />
<br />
=def. x is an occurrent and y is a plan and there is an agent z who is the agent_of x and is attempting in performing x to realize y and it is not the case that x realization_of y<br />
<br />
== derivation-like relations ==<br />
<br />
From [http://groups.google.com/group/bfo-discuss/browse_thread/thread/7929d436f64b8f04/428b25c2f72c3d60?#428b25c2f72c3d60 this thread].<br />
Related, section VI from http://ontology.buffalo.edu/smith/articles/16Days.pdf<br />
<br />
We need relations that parallel the definition of transformation and derivation, but for different configurations of identity and existence in time. Motivating examples are cases where entities retain identity as they become and cease to be part of something else (wheel/car, protein/protein complex).<br />
<br />
Here's an attempt, following the language in the relations paper.<br />
<br />
'''c assembled_from c1, c2, .. cn''' <br />
<br />
assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t<br />
<br />
'''c gains_part c1'''<br />
<br />
gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.<br />
<br />
'''c loses_part c1'''<br />
<br />
loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.<br />
<br />
'''c disassembles_into c1, c2,..., cn'''<br />
<br />
disassembles_into holds between material continuants when one ceases to exist at a certain time and some of its parts come to be self standing. Thus we will have axioms to the effect that from c disassembles_into c1 and c2 we can infer that c1 part_of c just before t, c2 part_of c just before t, etc, that the spatial region occupied by c contains the spatial regions of c1.. cn just before t, that c does not exist after t, and c1, c2.. exist at t.<br />
<br />
In terms of the "16 days" paper, assembly = unification, disassembly = separation.<br />
<br />
Another way to highlight the differences between the relations is this summary, in short <br />
hand. -> marks the temporal divide. If you don't see a variable on one <br />
side, the entity it denotes doesn't exist at that time. <br />
The {} is a kind of signature, even shorter version to emphasize the <br />
changes in existence. "," marks the temporal divide. "-" means <br />
something ceases to exist. "*-" means all denoted entities ceases to <br />
exist. "+" means something comes into existence. <br />
<br />
'''derivation''' {*-,+} <br><br />
a -> b c ''aka fission'' <br> <br />
b c -> a ''aka fusion''<br />
<br />
'''transformation''' {,} <br><br />
a,C(a) -> a,C'(a) <br />
<br />
'''gains part''' {,} <br><br />
a,b, not has_part(a,b) -> a,b, has_part(a,b) <br />
<br />
'''loses part''' {,} <br><br />
a,b, has_part(a,b) -> a,b, not has_part(a,b) <br />
<br />
'''unification/assembly''' {,+} <br><br />
a,b -> c, has_part(c,a),has_part(c,b) <br />
<br />
'''separation/disassembly''' {-,} <br><br />
c, has_part(c,a),has_part(c,b) -> a,b<br />
<br />
Note that Barry has suggested that derivation be revised so as to not imply that the entities that exist before the temporal divide cease to exist, but retaining that a new entity is created. If this comes to be, then we might imagine a hierarchy of relations<br />
<br />
* derives_from<br />
** fused_from<br />
** fissioned_from ''yes, lousy name''<br />
** assembled_from<br />
** disassembled_from <br />
<br />
gains_part and loses_part aren't derivation since no new entity is created. In that sense they are similar to transformation.<br />
<br />
=Errata in Relations paper=<br />
<br />
<br />
"C part_of C1 = [definition] for all c, t, if Cct then there is some c1 such that C1c1t and c part_of c1 at t.<br />
Note the 'all-some' structure of this definition, a structure which will recur in almost all the relations treated here.<br />
C part_of C1 defines a relational property of permanent parthood for Cs. It tells us that Cs, whenever they exist, exist as parts of C1s."<br />
<br />
it's not right to say "permanent" or "whenever they exist". Since entities change change type, more like "entities, whenever then instantiate C, are parts of C1s"<br />
<br />
<i>Alan Ruttenberg</i><br />
<br />
----<br />
<br />
Page R46.7, Contained_in relationship:<br />
<br />
The text says: "C1 overlap c2 at t =[definition] for some c, c part_of c1 at t and c part_of c2 at t."<br />
<br />
The first C1 is in upper case letters...i think it should be lower case.<br />
<br />
<i>Barry Smith</i><br />
<br />
=Background Material=<br />
<br />
* [http://obofoundry.org/ro/ Relation Ontology Home]<br />
* [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]<br />
* [http://ontology.buffalo.edu/smith/articles/cornucopia.pdf The Cornucopia of Formal-Ontological Relations]<br />
* [http://ontology.buffalo.edu/bfo/ BFO Home page]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=9759RO:Main Page2010-03-01T17:03:54Z<p>Alanr: /* Open issues */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
An RO expert meeting took place in May, 2008. See [[OntologyRelations]] for notes and presentations.<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
Mike And Chris' Relation Ontology Proposed (MACROP), a list targets relations is [[MACROP]]<br />
<br />
==Proposal regarding defined classes==<br />
<br />
We take 'type' as primitive; types are children of BFO categories, which are themselves types. In the definitions that follow we ignore the factor of time, which should however be made explicit according to the practices established in RO.<br />
<br />
extension =def. the class [collection, totality, set] of all instances of a type<br />
<br />
defined class =def. a class all of whose members instantiate the same type T, that is (1) not itself the extension of any type, (2) defined by means of a statement of necessary and sufficient conditions of the form 'A ... is a T which ...'.<br />
<br />
Example: all people holding violins in the La Scala Opera House at a certain time.<br />
<br />
composite class =def. a class all of whose members instantiate one or other of a number of types, T1, ... Tn, that is (1) not itself the extension of any type, (2) defined by means of a disjunction of statements giving necessary and sufficient conditions of the form 'A ... is either a T1 which ... or a Tn which ...'<br />
<br />
Example: all people or bacteria in the La Scala Opera House at a certain time; the pattern '...' exemplified by graphical instances and by morse code beeps.<br />
<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
On the logic of instance-level relations see also Bittner's paper [http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner_AO_07-60_printed.pdf here].<br />
<br />
==Proposed new type-level relations (posted by Melanie Courtot) ==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on <br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
Some of those are described in the [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo RO proposed] file.<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
:name: regulates<br />
:def: "A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process" []<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
:name: positively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
:name: negatively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
:ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_relations_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page <br />
:[https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]<br />
<br />
<br />
==Need for Specific Role Relations (BS)==<br />
<br />
x has a role => x is assigned the role e.g. in the protocol<br />
x realizes the role => x has the role<br />
x plays the role => x performs those actions which someone who has the role would perform if they were realizing it<br />
<br />
Someone who has a role can also play it<br />
But so also can someone who does not have the role, e.g. the doctor takes on the nurse role because the nurse is off sick.<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Note, the term 'homology' has had many uses. This is an attempt to formally define 'cladistic homology'. One possible informal way to define this: "similarity due to unbroken descent from a common ancestor" ('Developmental Plasticity and Evolution', Mary West-Eberhard (2003))<br />
<br />
<br />
<br />
x1 '''derived_by_direct_descent_from''' x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism<br />
<br />
- x1 is an anatomical structure<br />
<br />
- x1 '''part_of''' y1<br />
<br />
- y2 is an organism<br />
<br />
- x2 is an anatomical structure<br />
<br />
- x2 '''part_of''' y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of y2. *(see notes below)<br />
<br />
'''derived_by_descent_from''' is the instance level relation which is the transitive closure over '''derived_by_direct_descent_from'''<br />
<br />
From this we can define a type level relation:<br />
<br />
A in B ''derived_by_descent_from'' C in D :<br />
<br />
For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)<br />
<br />
a '''part_of''' b<br />
<br />
a '''derived_by_descent_from''' c<br />
<br />
c '''part_of''' d<br />
<br />
(Note – B must be a subclade of the clade genealogically descended from D)<br />
<br />
A1 in B1 ''homologous_to A2'' in B2<br />
<br />
iff<br />
<br />
exists A3, B3:<br />
<br />
A1 in B1 ''derived_by_descent_from'' A3 in B3<br />
<br />
&<br />
<br />
A2 in B2 ''derived_by_descent_from'' A3 in B3<br />
<br />
(Note B1 and B2 must both be subclades of the clade descending (in the genealogical sense) from D)<br />
<br />
[* This clause still needs some work]<br />
<br />
[* On the Phenoscape project list, Jim Balhoff added the following critique of this:<br />
<br />
Something that jumps out at me in the definition of derived_by_direct_descent_from:<br />
<br />
I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]<br />
<br />
[* DS: comment - I agree that reference to genetic sequence is (probably) unnecessary. Anyway, it is clear that the current formulation doesn't work: The morphology of my leg is determined by a partial copy of the genetic sequence that determined morphology of my father's arm. One possible alternative, deliberately ignoring genetics: Of all the anatomical structures in y2, x2 is the most morphologically similar to x1.<br />
]<br />
<br />
Note: Do we need to include time (exists & existed)? <br />
<br />
FN – just to be on the safe side we can include time – it's not obviously useful but it could block some objections and won't affect the logic.<br />
<br />
=== relation to what is in RO proposed ===<br />
<br />
Note that there are a number of synonyms for derived_by_descent_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language<br />
<br />
== Measurements ==<br />
<br />
At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation<br />
called is_measurement_of to relate a measurement to some entity. (I<br />
can't remember if these were the exact names we used).<br />
is_measurement_of is subpropertyOf is_about<br />
<br />
In the following we are discussing instance level relationships.<br />
<br />
* measurement_datum:<br />
** has_value:<br />
** in_units:<br />
** of_dimension:<br />
<br />
m1 type measurement:<br />
<br />
* m1 has_value 30^^xsd:float<br />
* m1 in_units_of degree_celsius (UO:0000027)<br />
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)<br />
<br />
(Unresolved: latter two are classes. I guess that means that<br />
in_units_of and of_dimension are annotation properties, which is a<br />
shame. Either that or degree_celsius and temperature_dimension are<br />
instances of some sort. Barry?)<br />
<br />
* room1 type site<br />
* room1 has_quality t1<br />
* t1 instance_of temperature (PATO:0000146)<br />
<br />
* m1 is_measurement_of t1<br />
<br />
It was left open exactly how to represent uncertainty in the<br />
measurement, but this was thought to be perhaps something associated<br />
with the instrument or with a collection of measurements, rather than<br />
what was associated with the individual measurement.<br />
<br />
Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z<br />
<br />
== Realization_of and Associated Relations == <br />
<br />
For OBI purposes there is a need for an instance-level relation between a plan (for instance a protocol) and the occurrent which realizes this plan.<br />
<br />
In its terms we might define, for example,<br />
<br />
x deviation_from y<br />
<br />
=def. x is an occurrent and y is a plan and there is an agent z who is the agent_of x and is attempting in performing x to realize y and it is not the case that x realization_of y<br />
<br />
== derivation-like relations ==<br />
<br />
From [http://groups.google.com/group/bfo-discuss/browse_thread/thread/7929d436f64b8f04/428b25c2f72c3d60?#428b25c2f72c3d60 this thread].<br />
Related, section VI from http://ontology.buffalo.edu/smith/articles/16Days.pdf<br />
<br />
We need relations that parallel the definition of transformation and derivation, but for different configurations of identity and existence in time. Motivating examples are cases where entities retain identity as they become and cease to be part of something else (wheel/car, protein/protein complex).<br />
<br />
Here's an attempt, following the language in the relations paper.<br />
<br />
'''c assembled_from c1, c2, .. cn''' <br />
<br />
assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t<br />
<br />
'''c gains_part c1'''<br />
<br />
gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.<br />
<br />
'''c loses_part c1'''<br />
<br />
loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.<br />
<br />
'''c disassembles_into c1, c2,..., cn'''<br />
<br />
disassembles_into holds between material continuants when one ceases to exist at a certain time and some of its parts come to be self standing. Thus we will have axioms to the effect that from c disassembles_into c1 and c2 we can infer that c1 part_of c just before t, c2 part_of c just before t, etc, that the spatial region occupied by c contains the spatial regions of c1.. cn just before t, that c does not exist after t, and c1, c2.. exist at t.<br />
<br />
In terms of the "16 days" paper, assembly = unification, disassembly = separation.<br />
<br />
Another way to highlight the differences between the relations is this summary, in short <br />
hand. -> marks the temporal divide. If you don't see a variable on one <br />
side, the entity it denotes doesn't exist at that time. <br />
The {} is a kind of signature, even shorter version to emphasize the <br />
changes in existence. "," marks the temporal divide. "-" means <br />
something ceases to exist. "*-" means all denoted entities ceases to <br />
exist. "+" means something comes into existence. <br />
<br />
'''derivation''' {*-,+} <br><br />
a -> b c ''aka fission'' <br> <br />
b c -> a ''aka fusion''<br />
<br />
'''transformation''' {,} <br><br />
a,C(a) -> a,C'(a) <br />
<br />
'''gains part''' {,} <br><br />
a,b, not has_part(a,b) -> a,b, has_part(a,b) <br />
<br />
'''loses part''' {,} <br><br />
a,b, has_part(a,b) -> a,b, not has_part(a,b) <br />
<br />
'''unification/assembly''' {,+} <br><br />
a,b -> c, has_part(c,a),has_part(c,b) <br />
<br />
'''separation/disassembly''' {-,} <br><br />
c, has_part(c,a),has_part(c,b) -> a,b<br />
<br />
Note that Barry has suggested that derivation be revised so as to not imply that the entities that exist before the temporal divide cease to exist, but retaining that a new entity is created. If this comes to be, then we might imagine a hierarchy of relations<br />
<br />
* derives_from<br />
** fused_from<br />
** fissioned_from ''yes, lousy name''<br />
** assembled_from<br />
** disassembled_from <br />
<br />
gains_part and loses_part aren't derivation since no new entity is created. In that sense they are similar to transformation.<br />
<br />
=Errata in Relations paper=<br />
<br />
=Background Material=<br />
<br />
* [http://obofoundry.org/ro/ Relation Ontology Home]<br />
* [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]<br />
* [http://ontology.buffalo.edu/smith/articles/cornucopia.pdf The Cornucopia of Formal-Ontological Relations]<br />
* [http://ontology.buffalo.edu/bfo/ BFO Home page]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=9758RO:Main Page2010-03-01T17:03:18Z<p>Alanr: /* Background Material */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
An RO expert meeting took place in May, 2008. See [[OntologyRelations]] for notes and presentations.<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
Mike And Chris' Relation Ontology Proposed (MACROP), a list targets relations is [[MACROP]]<br />
<br />
==Proposal regarding defined classes==<br />
<br />
We take 'type' as primitive; types are children of BFO categories, which are themselves types. In the definitions that follow we ignore the factor of time, which should however be made explicit according to the practices established in RO.<br />
<br />
extension =def. the class [collection, totality, set] of all instances of a type<br />
<br />
defined class =def. a class all of whose members instantiate the same type T, that is (1) not itself the extension of any type, (2) defined by means of a statement of necessary and sufficient conditions of the form 'A ... is a T which ...'.<br />
<br />
Example: all people holding violins in the La Scala Opera House at a certain time.<br />
<br />
composite class =def. a class all of whose members instantiate one or other of a number of types, T1, ... Tn, that is (1) not itself the extension of any type, (2) defined by means of a disjunction of statements giving necessary and sufficient conditions of the form 'A ... is either a T1 which ... or a Tn which ...'<br />
<br />
Example: all people or bacteria in the La Scala Opera House at a certain time; the pattern '...' exemplified by graphical instances and by morse code beeps.<br />
<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
On the logic of instance-level relations see also Bittner's paper [http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner_AO_07-60_printed.pdf here].<br />
<br />
==Proposed new type-level relations (posted by Melanie Courtot) ==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on <br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
Some of those are described in the [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo RO proposed] file.<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
:name: regulates<br />
:def: "A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process" []<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
:name: positively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
:name: negatively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
:ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_relations_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page <br />
:[https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]<br />
<br />
<br />
==Need for Specific Role Relations (BS)==<br />
<br />
x has a role => x is assigned the role e.g. in the protocol<br />
x realizes the role => x has the role<br />
x plays the role => x performs those actions which someone who has the role would perform if they were realizing it<br />
<br />
Someone who has a role can also play it<br />
But so also can someone who does not have the role, e.g. the doctor takes on the nurse role because the nurse is off sick.<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Note, the term 'homology' has had many uses. This is an attempt to formally define 'cladistic homology'. One possible informal way to define this: "similarity due to unbroken descent from a common ancestor" ('Developmental Plasticity and Evolution', Mary West-Eberhard (2003))<br />
<br />
<br />
<br />
x1 '''derived_by_direct_descent_from''' x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism<br />
<br />
- x1 is an anatomical structure<br />
<br />
- x1 '''part_of''' y1<br />
<br />
- y2 is an organism<br />
<br />
- x2 is an anatomical structure<br />
<br />
- x2 '''part_of''' y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of y2. *(see notes below)<br />
<br />
'''derived_by_descent_from''' is the instance level relation which is the transitive closure over '''derived_by_direct_descent_from'''<br />
<br />
From this we can define a type level relation:<br />
<br />
A in B ''derived_by_descent_from'' C in D :<br />
<br />
For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)<br />
<br />
a '''part_of''' b<br />
<br />
a '''derived_by_descent_from''' c<br />
<br />
c '''part_of''' d<br />
<br />
(Note – B must be a subclade of the clade genealogically descended from D)<br />
<br />
A1 in B1 ''homologous_to A2'' in B2<br />
<br />
iff<br />
<br />
exists A3, B3:<br />
<br />
A1 in B1 ''derived_by_descent_from'' A3 in B3<br />
<br />
&<br />
<br />
A2 in B2 ''derived_by_descent_from'' A3 in B3<br />
<br />
(Note B1 and B2 must both be subclades of the clade descending (in the genealogical sense) from D)<br />
<br />
[* This clause still needs some work]<br />
<br />
[* On the Phenoscape project list, Jim Balhoff added the following critique of this:<br />
<br />
Something that jumps out at me in the definition of derived_by_direct_descent_from:<br />
<br />
I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]<br />
<br />
[* DS: comment - I agree that reference to genetic sequence is (probably) unnecessary. Anyway, it is clear that the current formulation doesn't work: The morphology of my leg is determined by a partial copy of the genetic sequence that determined morphology of my father's arm. One possible alternative, deliberately ignoring genetics: Of all the anatomical structures in y2, x2 is the most morphologically similar to x1.<br />
]<br />
<br />
Note: Do we need to include time (exists & existed)? <br />
<br />
FN – just to be on the safe side we can include time – it's not obviously useful but it could block some objections and won't affect the logic.<br />
<br />
=== relation to what is in RO proposed ===<br />
<br />
Note that there are a number of synonyms for derived_by_descent_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language<br />
<br />
== Measurements ==<br />
<br />
At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation<br />
called is_measurement_of to relate a measurement to some entity. (I<br />
can't remember if these were the exact names we used).<br />
is_measurement_of is subpropertyOf is_about<br />
<br />
In the following we are discussing instance level relationships.<br />
<br />
* measurement_datum:<br />
** has_value:<br />
** in_units:<br />
** of_dimension:<br />
<br />
m1 type measurement:<br />
<br />
* m1 has_value 30^^xsd:float<br />
* m1 in_units_of degree_celsius (UO:0000027)<br />
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)<br />
<br />
(Unresolved: latter two are classes. I guess that means that<br />
in_units_of and of_dimension are annotation properties, which is a<br />
shame. Either that or degree_celsius and temperature_dimension are<br />
instances of some sort. Barry?)<br />
<br />
* room1 type site<br />
* room1 has_quality t1<br />
* t1 instance_of temperature (PATO:0000146)<br />
<br />
* m1 is_measurement_of t1<br />
<br />
It was left open exactly how to represent uncertainty in the<br />
measurement, but this was thought to be perhaps something associated<br />
with the instrument or with a collection of measurements, rather than<br />
what was associated with the individual measurement.<br />
<br />
Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z<br />
<br />
== Realization_of and Associated Relations == <br />
<br />
For OBI purposes there is a need for an instance-level relation between a plan (for instance a protocol) and the occurrent which realizes this plan.<br />
<br />
In its terms we might define, for example,<br />
<br />
x deviation_from y<br />
<br />
=def. x is an occurrent and y is a plan and there is an agent z who is the agent_of x and is attempting in performing x to realize y and it is not the case that x realization_of y<br />
<br />
== derivation-like relations ==<br />
<br />
From [http://groups.google.com/group/bfo-discuss/browse_thread/thread/7929d436f64b8f04/428b25c2f72c3d60?#428b25c2f72c3d60 this thread].<br />
Related, section VI from http://ontology.buffalo.edu/smith/articles/16Days.pdf<br />
<br />
We need relations that parallel the definition of transformation and derivation, but for different configurations of identity and existence in time. Motivating examples are cases where entities retain identity as they become and cease to be part of something else (wheel/car, protein/protein complex).<br />
<br />
Here's an attempt, following the language in the relations paper.<br />
<br />
'''c assembled_from c1, c2, .. cn''' <br />
<br />
assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t<br />
<br />
'''c gains_part c1'''<br />
<br />
gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.<br />
<br />
'''c loses_part c1'''<br />
<br />
loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.<br />
<br />
'''c disassembles_into c1, c2,..., cn'''<br />
<br />
disassembles_into holds between material continuants when one ceases to exist at a certain time and some of its parts come to be self standing. Thus we will have axioms to the effect that from c disassembles_into c1 and c2 we can infer that c1 part_of c just before t, c2 part_of c just before t, etc, that the spatial region occupied by c contains the spatial regions of c1.. cn just before t, that c does not exist after t, and c1, c2.. exist at t.<br />
<br />
In terms of the "16 days" paper, assembly = unification, disassembly = separation.<br />
<br />
Another way to highlight the differences between the relations is this summary, in short <br />
hand. -> marks the temporal divide. If you don't see a variable on one <br />
side, the entity it denotes doesn't exist at that time. <br />
The {} is a kind of signature, even shorter version to emphasize the <br />
changes in existence. "," marks the temporal divide. "-" means <br />
something ceases to exist. "*-" means all denoted entities ceases to <br />
exist. "+" means something comes into existence. <br />
<br />
'''derivation''' {*-,+} <br><br />
a -> b c ''aka fission'' <br> <br />
b c -> a ''aka fusion''<br />
<br />
'''transformation''' {,} <br><br />
a,C(a) -> a,C'(a) <br />
<br />
'''gains part''' {,} <br><br />
a,b, not has_part(a,b) -> a,b, has_part(a,b) <br />
<br />
'''loses part''' {,} <br><br />
a,b, has_part(a,b) -> a,b, not has_part(a,b) <br />
<br />
'''unification/assembly''' {,+} <br><br />
a,b -> c, has_part(c,a),has_part(c,b) <br />
<br />
'''separation/disassembly''' {-,} <br><br />
c, has_part(c,a),has_part(c,b) -> a,b<br />
<br />
Note that Barry has suggested that derivation be revised so as to not imply that the entities that exist before the temporal divide cease to exist, but retaining that a new entity is created. If this comes to be, then we might imagine a hierarchy of relations<br />
<br />
* derives_from<br />
** fused_from<br />
** fissioned_from ''yes, lousy name''<br />
** assembled_from<br />
** disassembled_from <br />
<br />
gains_part and loses_part aren't derivation since no new entity is created. In that sense they are similar to transformation.<br />
<br />
=Background Material=<br />
<br />
* [http://obofoundry.org/ro/ Relation Ontology Home]<br />
* [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]<br />
* [http://ontology.buffalo.edu/smith/articles/cornucopia.pdf The Cornucopia of Formal-Ontological Relations]<br />
* [http://ontology.buffalo.edu/bfo/ BFO Home page]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=From_BFO_to_IAO&diff=9021From BFO to IAO2009-07-19T23:13:54Z<p>Alanr: </p>
<hr />
<div>'''From Basic Formal Ontology to the Information Artifact Ontology'''<br />
<br />
Wednesday and Thursday, July 22-23, 2009<br />
<br />
Venue: [http://www.buffalo.edu/buildings/building?id=norton Norton 112], UB North Campus<br />
<br />
Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].<br />
<br />
Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time. <br />
<br />
'''Session 1: Wednesday 9am to 12.30pm''' <br />
*Barry Smith: introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative, <br />
<br />
'''Session 2: Wednesday 1.30pm to 5pm'''<br />
*Werner Ceusters: introduction to Referent Tracking, and its applications to the task of relating ontologies to instance data in ways useful to healthcare and biomedical research<br />
<br />
'''Session 3: Thursday 9am to 12.30pm''' <br />
*Alan Ruttenberg: Introduction to the [http://obi-ontology.org/ Ontology for Biomedical Investigations] (OBI) and the [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology] (IAO). OBI is a BFO-based integrated ontology for the description of life-science and clinical investigations. Its domain encompasses materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the investigation to the natural world as represented in other OBO ontologies. <br />
<br />
* IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created and consumed. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.<br />
<br />
* Attendees will finish these sessions with an understanding of upper level entities essential to read (and review) the ontologies in more detail, examples of how they can be applied, a picture of the current state of the ontology and of future work and be cognizant of issues that need to be resolved and perhaps primed to help solve them.<br />
<br />
'''Session 4: Thursday 1.30pm to 5pm'''<br />
*Discussion session (addressing a list of open questions and action items generated by the first 3 sessions)<br />
<br />
----<br />
'''Literature and Links'''<br />
<br />
* [http://obofoundry.org OBO Foundry]<br />
* [http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology]<br />
* [http://org.buffalo.edu/RTU/ Referent Tracking]<br />
* [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology]<br />
* [http://obi-ontology.org/ Ontology for Biomedical Investigations]<br />
<br />
----<br />
'''Faculty'''<br />
<br />
[http://org.buffalo.edu/ceusters/ Werner Ceusters] is Professor in the Psychiatry Department of the University at Buffalo (UB), Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Coordinator of Bioinformatics for the UB Health Science Faculties. <br />
<br />
[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org/ Science Commons]. His project, the Neurocommons, prototypes the use of<br />
Semantic Web technology for integrating and querying biomedical<br />
knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.<br />
<br />
[http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a Coordinating Editor of the OBO Foundry, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=From_BFO_to_IAO&diff=9020From BFO to IAO2009-07-19T22:06:11Z<p>Alanr: </p>
<hr />
<div>'''From Basic Formal Ontology to the Information Artifact Ontology'''<br />
<br />
Wednesday and Thursday, July 22-23, 2009<br />
<br />
Venue: [http://www.buffalo.edu/buildings/building?id=norton Norton 112], UB North Campus<br />
<br />
Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].<br />
<br />
Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time. <br />
<br />
'''Session 1: Wednesday 9am to 12.30pm''' <br />
*Barry Smith: introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative, <br />
<br />
'''Session 2: Wednesday 1.30pm to 5pm'''<br />
*Werner Ceusters: introduction to Referent Tracking, and its applications to the task of relating ontologies to instance data in ways useful to healthcare and biomedical research<br />
<br />
'''Session 3: Thursday 9am to 12.30pm''' <br />
*Alan Ruttenberg: Introduction to the [http://obi-ontology.org/ Ontology for Biomedical Investigations] (OBI) and the [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology] (IAO). OBI is a BFO-based integrated ontology for the description of life-science and clinical investigations and has as its domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies. <br />
<br />
* IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created and consumed. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.<br />
<br />
* Attendees will finish this session with a understanding of upper level entities essential to read (and review) the ontologies in more detail, examples of how they can be applied, a picture of the current state of the ontology and of future work and be cognizant of issues that need to be resolved and perhaps primed to help solve them.<br />
<br />
'''Session 4: Thursday 1.30pm to 5pm'''<br />
*Discussion session (addressing a list of open questions and action items generated by the first 3 sessions)<br />
<br />
----<br />
'''Literature and Links'''<br />
<br />
* [http://obofoundry.org OBO Foundry]<br />
* [http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology]<br />
* [http://org.buffalo.edu/RTU/ Referent Tracking]<br />
* [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology]<br />
* [http://obi-ontology.org/ Ontology for Biomedical Investigations]<br />
<br />
----<br />
'''Faculty'''<br />
<br />
[http://org.buffalo.edu/ceusters/ Werner Ceusters] is Professor in the Psychiatry Department of the University at Buffalo (UB), Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Coordinator of Bioinformatics for the UB Health Science Faculties. <br />
<br />
[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org/ Science Commons]. His project, the Neurocommons, prototypes the use of<br />
Semantic Web technology for integrating and querying biomedical<br />
knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.<br />
<br />
[http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a Coordinating Editor of the OBO Foundry, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=From_BFO_to_IAO&diff=9019From BFO to IAO2009-07-19T22:04:56Z<p>Alanr: </p>
<hr />
<div>'''From Basic Formal Ontology to the Information Artifact Ontology'''<br />
<br />
Wednesday and Thursday, July 22-23, 2009<br />
<br />
Venue: [http://www.buffalo.edu/buildings/building?id=norton Norton 112], UB North Campus<br />
<br />
Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].<br />
<br />
Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time. <br />
<br />
'''Session 1: Wednesday 9am to 12.30pm''' <br />
*Barry Smith: introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative, <br />
<br />
'''Session 2: Wednesday 1.30pm to 5pm'''<br />
*Werner Ceusters: introduction to Referent Tracking, and its applications to the task of relating ontologies to instance data in ways useful to healthcare and biomedical research<br />
<br />
'''Session 3: Thursday 9am to 12.30pm''' <br />
*Alan Ruttenberg: Introduction to the [http://obi-ontology.org/ Ontology for Biomedical Investigations] (OBI) and the [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology] (IAO). OBI is a BFO-based integrated ontology for the description of life-science and clinical investigations and has as it's domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies. <br />
<br />
* IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created and consumed. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.<br />
<br />
* Attendees will finish this session with a understanding of upper level entities essential to read (and review) the ontologies in more detail, examples of how they can be applied, a picture of the current state of the ontology and of future work and be cognizant of issues that need to be resolved and perhaps primed to help solve them.<br />
<br />
'''Session 4: Thursday 1.30pm to 5pm'''<br />
*Discussion session (addressing a list of open questions and action items generated by the first 3 sessions)<br />
<br />
----<br />
'''Literature and Links'''<br />
<br />
* [http://obofoundry.org OBO Foundry]<br />
* [http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology]<br />
* [http://org.buffalo.edu/RTU/ Referent Tracking]<br />
* [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology]<br />
* [http://obi-ontology.org/ Ontology for Biomedical Investigations]<br />
<br />
----<br />
'''Faculty'''<br />
<br />
[http://org.buffalo.edu/ceusters/ Werner Ceusters] is Professor in the Psychiatry Department of the University at Buffalo (UB), Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Coordinator of Bioinformatics for the UB Health Science Faculties. <br />
<br />
[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org/ Science Commons]. His project, the Neurocommons, prototypes the use of<br />
Semantic Web technology for integrating and querying biomedical<br />
knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.<br />
<br />
[http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a Coordinating Editor of the OBO Foundry, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=From_BFO_to_IAO&diff=9018From BFO to IAO2009-07-19T21:58:31Z<p>Alanr: </p>
<hr />
<div>'''From Basic Formal Ontology to the Information Artifact Ontology'''<br />
<br />
Wednesday and Thursday, July 22-23, 2009<br />
<br />
Venue: [http://www.buffalo.edu/buildings/building?id=norton Norton 112], UB North Campus<br />
<br />
Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].<br />
<br />
Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time. <br />
<br />
'''Session 1: Wednesday 9am to 12.30pm''' <br />
*Barry Smith: introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative, <br />
<br />
'''Session 2: Wednesday 1.30pm to 5pm'''<br />
*Werner Ceusters: introduction to Referent Tracking, and its applications to the task of relating ontologies to instance data in ways useful to healthcare and biomedical research<br />
<br />
'''Session 3: Thursday 9am to 12.30pm''' <br />
*Alan Ruttenberg: introduction to the Ontology for Biomedical Investigations(OBI) and the Information Artifact Ontology(IAO). OBI is a BFO-based integrated ontology for the description of life-science and clinical investigations and has as it's domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies. <br />
<br />
* IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.<br />
<br />
* Attendees should finish this session with a understanding of upper level entities essential to read the ontologies in more detail, a picture of that current state of the ontology, a picture of expected future work, being cognizant of issues that need to be resolved and perhaps primed to help solve them.<br />
<br />
'''Session 4: Thursday 1.30pm to 5pm'''<br />
*Discussion session (addressing a list of open questions and action items generated by the first 3 sessions)<br />
<br />
----<br />
'''Literature and Links'''<br />
<br />
[http://obofoundry.org OBO Foundry]<br />
<br />
[http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology]<br />
<br />
[http://org.buffalo.edu/RTU/ Referent Tracking]<br />
<br />
[http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology]<br />
----<br />
'''Faculty'''<br />
<br />
[http://org.buffalo.edu/ceusters/ Werner Ceusters] is Professor in the Psychiatry Department of the University at Buffalo (UB), Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Coordinator of Bioinformatics for the UB Health Science Faculties. <br />
<br />
[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org/ Science Commons]. His project, the Neurocommons, prototypes the use of<br />
Semantic Web technology for integrating and querying biomedical<br />
knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.<br />
<br />
[http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a Coordinating Editor of the OBO Foundry, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=From_BFO_to_IAO&diff=9017From BFO to IAO2009-07-19T21:58:13Z<p>Alanr: </p>
<hr />
<div>'''From Basic Formal Ontology to the Information Artifact Ontology'''<br />
<br />
Wednesday and Thursday, July 22-23, 2009<br />
<br />
Venue: [http://www.buffalo.edu/buildings/building?id=norton Norton 112], UB North Campus<br />
<br />
Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].<br />
<br />
Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time. <br />
<br />
'''Session 1: Wednesday 9am to 12.30pm''' <br />
*Barry Smith: introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative, <br />
<br />
'''Session 2: Wednesday 1.30pm to 5pm'''<br />
*Werner Ceusters: introduction to Referent Tracking, and its applications to the task of relating ontologies to instance data in ways useful to healthcare and biomedical research<br />
<br />
'''Session 3: Thursday 9am to 12.30pm''' <br />
*Alan Ruttenberg: introduction to the Ontology for Biomedical Investigations(OBI) and the Information Artifact Ontology(IAO). OBI is a BFO-based integrated ontology for the description of life-science and clinical investigations and has as it's domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies. <br />
<br />
IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.<br />
<br />
Attendees should finish this session with a understanding of upper level entities essential to read the ontologies in more detail, a picture of that current state of the ontology, a picture of expected future work, being cognizant of issues that need to be resolved and perhaps primed to help solve them.<br />
<br />
'''Session 4: Thursday 1.30pm to 5pm'''<br />
*Discussion session (addressing a list of open questions and action items generated by the first 3 sessions)<br />
<br />
----<br />
'''Literature and Links'''<br />
<br />
[http://obofoundry.org OBO Foundry]<br />
<br />
[http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology]<br />
<br />
[http://org.buffalo.edu/RTU/ Referent Tracking]<br />
<br />
[http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology]<br />
----<br />
'''Faculty'''<br />
<br />
[http://org.buffalo.edu/ceusters/ Werner Ceusters] is Professor in the Psychiatry Department of the University at Buffalo (UB), Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Coordinator of Bioinformatics for the UB Health Science Faculties. <br />
<br />
[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org/ Science Commons]. His project, the Neurocommons, prototypes the use of<br />
Semantic Web technology for integrating and querying biomedical<br />
knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.<br />
<br />
[http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a Coordinating Editor of the OBO Foundry, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=8782RO:Main Page2009-05-11T05:00:03Z<p>Alanr: /* derivation-like relations */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
An RO expert meeting took place in May, 2008. See [[OntologyRelations]] for notes and presentations.<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
Mike And Chris' Relation Ontology Proposed (MACROP), a list targets relations is [[MACROP]]<br />
<br />
==Proposal regarding defined classes==<br />
<br />
We take 'type' as primitive; types are children of BFO categories, which are themselves types. In the definitions that follow we ignore the factor of time, which should however be made explicit according to the practices established in RO.<br />
<br />
extension =def. the class [collection, totality, set] of all instances of a type<br />
<br />
defined class =def. a class all of whose members instantiate the same type T, that is (1) not itself the extension of any type, (2) defined by means of a statement of necessary and sufficient conditions of the form 'A ... is a T which ...'.<br />
<br />
Example: all people holding violins in the La Scala Opera House at a certain time.<br />
<br />
composite class =def. a class all of whose members instantiate one or other of a number of types, T1, ... Tn, that is (1) not itself the extension of any type, (2) defined by means of a disjunction of statements giving necessary and sufficient conditions of the form 'A ... is either a T1 which ... or a Tn which ...'<br />
<br />
Example: all people or bacteria in the La Scala Opera House at a certain time; the pattern '...' exemplified by graphical instances and by morse code beeps.<br />
<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
On the logic of instance-level relations see also Bittner's paper [http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner_AO_07-60_printed.pdf here].<br />
<br />
==Proposed new type-level relations (posted by Melanie Courtot) ==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on <br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
Some of those are described in the [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo RO proposed] file.<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
:name: regulates<br />
:def: "A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process" []<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
:name: positively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
:name: negatively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
:ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_relations_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page <br />
:[https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]<br />
<br />
<br />
==Need for Specific Role Relations (BS)==<br />
<br />
x has a role => x is assigned the role e.g. in the protocol<br />
x realizes the role => x has the role<br />
x plays the role => x performs those actions which someone who has the role would perform if they were realizing it<br />
<br />
Someone who has a role can also play it<br />
But so also can someone who does not have the role, e.g. the doctor takes on the nurse role because the nurse is off sick.<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
x1 '''directly_descends_from''' x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism<br />
<br />
- x1 is an anatomical structure<br />
<br />
- x1 '''part_of''' y1<br />
<br />
- y2 is an organism<br />
<br />
- x2 is an anatomical structure<br />
<br />
- x2 '''part_of''' y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of. *(see notes below)<br />
<br />
'''descends_from''' is the instance level relation which is the transitive closure over '''directly_descends_from'''<br />
<br />
From this we can define a type level relation:<br />
<br />
A in B ''descends_from'' C in D :<br />
<br />
For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)<br />
<br />
a '''part_of''' b<br />
<br />
a '''descends_from''' c<br />
<br />
c '''part_of''' d<br />
<br />
(Note – B must be a subclade of the clade genealogically descended from D)<br />
<br />
A1 in B1 ''homologous_to A2'' in B2<br />
<br />
iff<br />
<br />
exists A3, B3:<br />
<br />
A1 in B1 ''descends_from A3'' in B3<br />
<br />
&<br />
<br />
A2 in B2 ''descends_from'' A3 in B3<br />
<br />
(Note B1 and B2 must both be subclades of the clade descending (in the genealogical sense) from D)<br />
<br />
[* This clause still needs some work]<br />
<br />
[* On the Phenoscape project list, Jim Balhoff added the following critique of this:<br />
<br />
Something that jumps out at me in the definition of directly_descends_from:<br />
<br />
I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]<br />
<br />
[* DS: comment - I agree that reference to genetic sequence is (probably) unnecessary. Anyway, it is clear that the current formulation doesn't work: The morphology of my leg is determined by a partial copy of the genetic sequence that determined morphology of my father's arm. One possible alternative, deliberately ignoring genetics: Of all the anatomical structures in y2, x2 is the most morphologically similar to x1.<br />
]<br />
<br />
Note: Do we need to include time (exists & existed)? <br />
<br />
FN – just to be on the safe side we can include time – it's not obviously useful but it could block some objections and won't affect the logic.<br />
<br />
=== relation to what is in RO proposed ===<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language<br />
<br />
== Measurements ==<br />
<br />
At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation<br />
called is_measurement_of to relate a measurement to some entity. (I<br />
can't remember if these were the exact names we used).<br />
is_measurement_of is subpropertyOf is_about<br />
<br />
In the following we are discussing instance level relationships.<br />
<br />
* measurement_datum:<br />
** has_value:<br />
** in_units:<br />
** of_dimension:<br />
<br />
m1 type measurement:<br />
<br />
* m1 has_value 30^^xsd:float<br />
* m1 in_units_of degree_celsius (UO:0000027)<br />
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)<br />
<br />
(Unresolved: latter two are classes. I guess that means that<br />
in_units_of and of_dimension are annotation properties, which is a<br />
shame. Either that or degree_celsius and temperature_dimension are<br />
instances of some sort. Barry?)<br />
<br />
* room1 type site<br />
* room1 has_quality t1<br />
* t1 instance_of temperature (PATO:0000146)<br />
<br />
* m1 is_measurement_of t1<br />
<br />
It was left open exactly how to represent uncertainty in the<br />
measurement, but this was thought to be perhaps something associated<br />
with the instrument or with a collection of measurements, rather than<br />
what was associated with the individual measurement.<br />
<br />
Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z<br />
<br />
== Realization_of and Associated Relations == <br />
<br />
For OBI purposes there is a need for an instance-level relation between a plan (for instance a protocol) and the occurrent which realizes this plan.<br />
<br />
In its terms we might define, for example,<br />
<br />
x deviation_from y<br />
<br />
=def. x is an occurrent and y is a plan and there is an agent z who is the agent_of x and is attempting in performing x to realize y and it is not the case that x realization_of y<br />
<br />
== derivation-like relations ==<br />
<br />
From [http://groups.google.com/group/bfo-discuss/browse_thread/thread/7929d436f64b8f04/428b25c2f72c3d60?#428b25c2f72c3d60 this thread].<br />
Related, section VI from http://ontology.buffalo.edu/smith/articles/16Days.pdf<br />
<br />
We need relations that parallel the definition of transformation and derivation, but for different configurations of identity and existence in time. Motivating examples are cases where entities retain identity as they become and cease to be part of something else (wheel/car, protein/protein complex).<br />
<br />
Here's an attempt, following the language in the relations paper.<br />
<br />
'''c assembled_from c1, c2, .. cn''' <br />
<br />
assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t<br />
<br />
'''c gains_part c1'''<br />
<br />
gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.<br />
<br />
'''c loses_part c1'''<br />
<br />
loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.<br />
<br />
'''c disassembles_into c1, c2,..., cn'''<br />
<br />
disassembles_into holds between material continuants when one ceases to exist at a certain time and some of its parts come to be self standing. Thus we will have axioms to the effect that from c disassembles_into c1 and c2 we can infer that c1 part_of c just before t, c2 part_of c just before t, etc, that the spatial region occupied by c contains the spatial regions of c1.. cn just before t, that c does not exist after t, and c1, c2.. exist at t.<br />
<br />
In terms of the "16 days" paper, assembly = unification, disassembly = separation.<br />
<br />
Another way to highlight the differences between the relations is this summary, in short <br />
hand. -> marks the temporal divide. If you don't see a variable on one <br />
side, the entity it denotes doesn't exist at that time. <br />
The {} is a kind of signature, even shorter version to emphasize the <br />
changes in existence. "," marks the temporal divide. "-" means <br />
something ceases to exist. "*-" means all denoted entities ceases to <br />
exist. "+" means something comes into existence. <br />
<br />
'''derivation''' {*-,+} <br><br />
a -> b c ''aka fission'' <br> <br />
b c -> a ''aka fusion''<br />
<br />
'''transformation''' {,} <br><br />
a,C(a) -> a,C'(a) <br />
<br />
'''gains part''' {,} <br><br />
a,b, not has_part(a,b) -> a,b, has_part(a,b) <br />
<br />
'''loses part''' {,} <br><br />
a,b, has_part(a,b) -> a,b, not has_part(a,b) <br />
<br />
'''unification/assembly''' {,+} <br><br />
a,b -> c, has_part(c,a),has_part(c,b) <br />
<br />
'''separation/disassembly''' {-,} <br><br />
c, has_part(c,a),has_part(c,b) -> a,b<br />
<br />
Note that Barry has suggested that derivation be revised so as to not imply that the entities that exist before the temporal divide cease to exist, but retaining that a new entity is created. If this comes to be, then we might imagine a hierarchy of relations<br />
<br />
* derives_from<br />
** fused_from<br />
** fissioned_from ''yes, lousy name''<br />
** assembled_from<br />
** disassembled_from <br />
<br />
gains_part and loses_part aren't derivation since no new entity is created. In that sense they are similar to transformation.<br />
<br />
=Background Material=<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home]<br />
<br />
[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=8781RO:Main Page2009-05-11T04:58:29Z<p>Alanr: /* derivation-like relations */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
An RO expert meeting took place in May, 2008. See [[OntologyRelations]] for notes and presentations.<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
Mike And Chris' Relation Ontology Proposed (MACROP), a list targets relations is [[MACROP]]<br />
<br />
==Proposal regarding defined classes==<br />
<br />
We take 'type' as primitive; types are children of BFO categories, which are themselves types. In the definitions that follow we ignore the factor of time, which should however be made explicit according to the practices established in RO.<br />
<br />
extension =def. the class [collection, totality, set] of all instances of a type<br />
<br />
defined class =def. a class all of whose members instantiate the same type T, that is (1) not itself the extension of any type, (2) defined by means of a statement of necessary and sufficient conditions of the form 'A ... is a T which ...'.<br />
<br />
Example: all people holding violins in the La Scala Opera House at a certain time.<br />
<br />
composite class =def. a class all of whose members instantiate one or other of a number of types, T1, ... Tn, that is (1) not itself the extension of any type, (2) defined by means of a disjunction of statements giving necessary and sufficient conditions of the form 'A ... is either a T1 which ... or a Tn which ...'<br />
<br />
Example: all people or bacteria in the La Scala Opera House at a certain time; the pattern '...' exemplified by graphical instances and by morse code beeps.<br />
<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
On the logic of instance-level relations see also Bittner's paper [http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner_AO_07-60_printed.pdf here].<br />
<br />
==Proposed new type-level relations (posted by Melanie Courtot) ==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on <br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
Some of those are described in the [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo RO proposed] file.<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
:name: regulates<br />
:def: "A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process" []<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
:name: positively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
:name: negatively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
:ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_relations_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page <br />
:[https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]<br />
<br />
<br />
==Need for Specific Role Relations (BS)==<br />
<br />
x has a role => x is assigned the role e.g. in the protocol<br />
x realizes the role => x has the role<br />
x plays the role => x performs those actions which someone who has the role would perform if they were realizing it<br />
<br />
Someone who has a role can also play it<br />
But so also can someone who does not have the role, e.g. the doctor takes on the nurse role because the nurse is off sick.<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
x1 '''directly_descends_from''' x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism<br />
<br />
- x1 is an anatomical structure<br />
<br />
- x1 '''part_of''' y1<br />
<br />
- y2 is an organism<br />
<br />
- x2 is an anatomical structure<br />
<br />
- x2 '''part_of''' y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of. *(see notes below)<br />
<br />
'''descends_from''' is the instance level relation which is the transitive closure over '''directly_descends_from'''<br />
<br />
From this we can define a type level relation:<br />
<br />
A in B ''descends_from'' C in D :<br />
<br />
For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)<br />
<br />
a '''part_of''' b<br />
<br />
a '''descends_from''' c<br />
<br />
c '''part_of''' d<br />
<br />
(Note – B must be a subclade of the clade genealogically descended from D)<br />
<br />
A1 in B1 ''homologous_to A2'' in B2<br />
<br />
iff<br />
<br />
exists A3, B3:<br />
<br />
A1 in B1 ''descends_from A3'' in B3<br />
<br />
&<br />
<br />
A2 in B2 ''descends_from'' A3 in B3<br />
<br />
(Note B1 and B2 must both be subclades of the clade descending (in the genealogical sense) from D)<br />
<br />
[* This clause still needs some work]<br />
<br />
[* On the Phenoscape project list, Jim Balhoff added the following critique of this:<br />
<br />
Something that jumps out at me in the definition of directly_descends_from:<br />
<br />
I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]<br />
<br />
[* DS: comment - I agree that reference to genetic sequence is (probably) unnecessary. Anyway, it is clear that the current formulation doesn't work: The morphology of my leg is determined by a partial copy of the genetic sequence that determined morphology of my father's arm. One possible alternative, deliberately ignoring genetics: Of all the anatomical structures in y2, x2 is the most morphologically similar to x1.<br />
]<br />
<br />
Note: Do we need to include time (exists & existed)? <br />
<br />
FN – just to be on the safe side we can include time – it's not obviously useful but it could block some objections and won't affect the logic.<br />
<br />
=== relation to what is in RO proposed ===<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language<br />
<br />
== Measurements ==<br />
<br />
At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation<br />
called is_measurement_of to relate a measurement to some entity. (I<br />
can't remember if these were the exact names we used).<br />
is_measurement_of is subpropertyOf is_about<br />
<br />
In the following we are discussing instance level relationships.<br />
<br />
* measurement_datum:<br />
** has_value:<br />
** in_units:<br />
** of_dimension:<br />
<br />
m1 type measurement:<br />
<br />
* m1 has_value 30^^xsd:float<br />
* m1 in_units_of degree_celsius (UO:0000027)<br />
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)<br />
<br />
(Unresolved: latter two are classes. I guess that means that<br />
in_units_of and of_dimension are annotation properties, which is a<br />
shame. Either that or degree_celsius and temperature_dimension are<br />
instances of some sort. Barry?)<br />
<br />
* room1 type site<br />
* room1 has_quality t1<br />
* t1 instance_of temperature (PATO:0000146)<br />
<br />
* m1 is_measurement_of t1<br />
<br />
It was left open exactly how to represent uncertainty in the<br />
measurement, but this was thought to be perhaps something associated<br />
with the instrument or with a collection of measurements, rather than<br />
what was associated with the individual measurement.<br />
<br />
Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z<br />
<br />
== Realization_of and Associated Relations == <br />
<br />
For OBI purposes there is a need for an instance-level relation between a plan (for instance a protocol) and the occurrent which realizes this plan.<br />
<br />
In its terms we might define, for example,<br />
<br />
x deviation_from y<br />
<br />
=def. x is an occurrent and y is a plan and there is an agent z who is the agent_of x and is attempting in performing x to realize y and it is not the case that x realization_of y<br />
<br />
== derivation-like relations ==<br />
<br />
From [http://groups.google.com/group/bfo-discuss/browse_thread/thread/7929d436f64b8f04/428b25c2f72c3d60?#428b25c2f72c3d60 this thread].<br />
Related, section VI from http://ontology.buffalo.edu/smith/articles/16Days.pdf<br />
<br />
We need relations that parallel the definition of transformation and derivation, but for different configurations of identity and existence in time. Motivating examples are cases where entities retain identity as they become and cease to be part of something else (wheel/car, protein/protein complex).<br />
<br />
Here's an attempt, following the language in the relations paper.<br />
<br />
'''c assembled_from c1, c2, .. cn''' <br />
<br />
assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t<br />
<br />
<br />
'''c gains_part c1'''<br />
<br />
gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.<br />
<br />
'''c loses_part c1'''<br />
<br />
loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.<br />
<br />
'''c disassembles_into c1, c2,..., cn'''<br />
<br />
disassembles_into holds between material continuants when one ceases to exist at a certain time and some of its parts come to be self standing. Thus we will have axioms to the effect that from c disassembles_into c1 and c2 we can infer that c1 part_of c just before t, c2 part_of c just before t, etc, that the spatial region occupied by c contains the spatial regions of c1.. cn just before t, that c does not exist after t, and c1, c2.. exist at t.<br />
<br />
In terms of the "16 days" paper, assembly = unification, disassembly = separation.<br />
<br />
Another way to highlight the differences between the relations is this summary, in short <br />
hand. -> marks the temporal divide. If you don't see a variable on one <br />
side, the entity it denotes doesn't exist at that time. <br />
The {} is a kind of signature, even shorter version to emphasize the <br />
changes in existence. "," marks the temporal divide. "-" means <br />
something ceases to exist. "*-" means all denoted entities ceases to <br />
exist. "+" means something comes into existence. <br />
<br />
'''derivation''' {*-,+} <br><br />
a -> b c ''aka fission'' <br> <br />
b c -> a ''aka fusion''<br />
<br />
'''transformation''' {,} <br><br />
a,C(a) -> a,C'(a) <br />
<br />
'''gains part''' {,} <br><br />
a,b, not has_part(a,b) -> a,b, has_part(a,b) <br />
<br />
'''loses part''' {,} <br><br />
a,b, has_part(a,b) -> a,b, not has_part(a,b) <br />
<br />
'''unification/assembly''' {,+} <br><br />
a,b -> c, has_part(c,a),has_part(c,b) <br />
<br />
'''separation/disassembly''' {-,} <br><br />
c, has_part(c,a),has_part(c,b) -> a,b<br />
<br />
Note that Barry has suggested that derivation be revised so as to not imply that the entities that exist before the temporal divide cease to exist, but retaining that a new entity is created. If this comes to be, then we might imagine a hierarchy of relations<br />
<br />
* derives_from<br />
** fused_from<br />
** fissioned_from ''yes, lousy name''<br />
** assembled_from<br />
** disassembled_from <br />
<br />
gains_part and loses_part aren't derivation since no new entity is created. In that sense they are similar to transformation.<br />
<br />
=Background Material=<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home]<br />
<br />
[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=8780RO:Main Page2009-05-11T04:55:23Z<p>Alanr: /* Realization_of and Associated Relations */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
An RO expert meeting took place in May, 2008. See [[OntologyRelations]] for notes and presentations.<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
Mike And Chris' Relation Ontology Proposed (MACROP), a list targets relations is [[MACROP]]<br />
<br />
==Proposal regarding defined classes==<br />
<br />
We take 'type' as primitive; types are children of BFO categories, which are themselves types. In the definitions that follow we ignore the factor of time, which should however be made explicit according to the practices established in RO.<br />
<br />
extension =def. the class [collection, totality, set] of all instances of a type<br />
<br />
defined class =def. a class all of whose members instantiate the same type T, that is (1) not itself the extension of any type, (2) defined by means of a statement of necessary and sufficient conditions of the form 'A ... is a T which ...'.<br />
<br />
Example: all people holding violins in the La Scala Opera House at a certain time.<br />
<br />
composite class =def. a class all of whose members instantiate one or other of a number of types, T1, ... Tn, that is (1) not itself the extension of any type, (2) defined by means of a disjunction of statements giving necessary and sufficient conditions of the form 'A ... is either a T1 which ... or a Tn which ...'<br />
<br />
Example: all people or bacteria in the La Scala Opera House at a certain time; the pattern '...' exemplified by graphical instances and by morse code beeps.<br />
<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
On the logic of instance-level relations see also Bittner's paper [http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner_AO_07-60_printed.pdf here].<br />
<br />
==Proposed new type-level relations (posted by Melanie Courtot) ==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on <br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
Some of those are described in the [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo RO proposed] file.<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
:name: regulates<br />
:def: "A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process" []<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
:name: positively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
:name: negatively_regulates<br />
:def: "A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process"<br />
:is_a: OBO_REL:regulates<br />
:transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
:ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_relations_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page <br />
:[https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]<br />
<br />
<br />
==Need for Specific Role Relations (BS)==<br />
<br />
x has a role => x is assigned the role e.g. in the protocol<br />
x realizes the role => x has the role<br />
x plays the role => x performs those actions which someone who has the role would perform if they were realizing it<br />
<br />
Someone who has a role can also play it<br />
But so also can someone who does not have the role, e.g. the doctor takes on the nurse role because the nurse is off sick.<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
x1 '''directly_descends_from''' x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism<br />
<br />
- x1 is an anatomical structure<br />
<br />
- x1 '''part_of''' y1<br />
<br />
- y2 is an organism<br />
<br />
- x2 is an anatomical structure<br />
<br />
- x2 '''part_of''' y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of. *(see notes below)<br />
<br />
'''descends_from''' is the instance level relation which is the transitive closure over '''directly_descends_from'''<br />
<br />
From this we can define a type level relation:<br />
<br />
A in B ''descends_from'' C in D :<br />
<br />
For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)<br />
<br />
a '''part_of''' b<br />
<br />
a '''descends_from''' c<br />
<br />
c '''part_of''' d<br />
<br />
(Note – B must be a subclade of the clade genealogically descended from D)<br />
<br />
A1 in B1 ''homologous_to A2'' in B2<br />
<br />
iff<br />
<br />
exists A3, B3:<br />
<br />
A1 in B1 ''descends_from A3'' in B3<br />
<br />
&<br />
<br />
A2 in B2 ''descends_from'' A3 in B3<br />
<br />
(Note B1 and B2 must both be subclades of the clade descending (in the genealogical sense) from D)<br />
<br />
[* This clause still needs some work]<br />
<br />
[* On the Phenoscape project list, Jim Balhoff added the following critique of this:<br />
<br />
Something that jumps out at me in the definition of directly_descends_from:<br />
<br />
I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]<br />
<br />
[* DS: comment - I agree that reference to genetic sequence is (probably) unnecessary. Anyway, it is clear that the current formulation doesn't work: The morphology of my leg is determined by a partial copy of the genetic sequence that determined morphology of my father's arm. One possible alternative, deliberately ignoring genetics: Of all the anatomical structures in y2, x2 is the most morphologically similar to x1.<br />
]<br />
<br />
Note: Do we need to include time (exists & existed)? <br />
<br />
FN – just to be on the safe side we can include time – it's not obviously useful but it could block some objections and won't affect the logic.<br />
<br />
=== relation to what is in RO proposed ===<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language<br />
<br />
== Measurements ==<br />
<br />
At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation<br />
called is_measurement_of to relate a measurement to some entity. (I<br />
can't remember if these were the exact names we used).<br />
is_measurement_of is subpropertyOf is_about<br />
<br />
In the following we are discussing instance level relationships.<br />
<br />
* measurement_datum:<br />
** has_value:<br />
** in_units:<br />
** of_dimension:<br />
<br />
m1 type measurement:<br />
<br />
* m1 has_value 30^^xsd:float<br />
* m1 in_units_of degree_celsius (UO:0000027)<br />
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)<br />
<br />
(Unresolved: latter two are classes. I guess that means that<br />
in_units_of and of_dimension are annotation properties, which is a<br />
shame. Either that or degree_celsius and temperature_dimension are<br />
instances of some sort. Barry?)<br />
<br />
* room1 type site<br />
* room1 has_quality t1<br />
* t1 instance_of temperature (PATO:0000146)<br />
<br />
* m1 is_measurement_of t1<br />
<br />
It was left open exactly how to represent uncertainty in the<br />
measurement, but this was thought to be perhaps something associated<br />
with the instrument or with a collection of measurements, rather than<br />
what was associated with the individual measurement.<br />
<br />
Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z<br />
<br />
== Realization_of and Associated Relations == <br />
<br />
For OBI purposes there is a need for an instance-level relation between a plan (for instance a protocol) and the occurrent which realizes this plan.<br />
<br />
In its terms we might define, for example,<br />
<br />
x deviation_from y<br />
<br />
=def. x is an occurrent and y is a plan and there is an agent z who is the agent_of x and is attempting in performing x to realize y and it is not the case that x realization_of y<br />
<br />
== derivation-like relations ==<br />
<br />
From [http://groups.google.com/group/bfo-discuss/browse_thread/thread/7929d436f64b8f04/428b25c2f72c3d60?#428b25c2f72c3d60 this thread].<br />
Related, section VI from http://ontology.buffalo.edu/smith/articles/16Days.pdf<br />
<br />
We need relations, I think, that parallel the definition of transformation and derivation, but for different configurations of identity and existence in time. Here's an attempt, following the language in the relations paper.<br />
<br />
'''c assembled_from c1, c2, .. cn''' <br />
<br />
assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t<br />
<br />
'''c gains_part c1'''<br />
<br />
gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.<br />
<br />
'''c loses_part c1'''<br />
<br />
loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.<br />
<br />
'''c disassembles_into c1, c2,..., cn'''<br />
<br />
disassembles_into holds between material continuants when one ceases to exist at a certain time and some of its parts come to be self standing. Thus we will have axioms to the effect that from c disassembles_into c1 and c2 we can infer that c1 part_of c just before t, c2 part_of c just before t, etc, that the spatial region occupied by c contains the spatial regions of c1.. cn just before t, that c does not exist after t, and c1, c2.. exist at t.<br />
<br />
In terms of the "16 days" paper, assembly = unification, disassembly = separation.<br />
<br />
Another way to highlight the differences between the relations is this summary, in short <br />
hand. -> marks the temporal divide. If you don't see a variable on one <br />
side, the entity it denotes doesn't exist at that time. <br />
The {} is a kind of signature, even shorter version to emphasize the <br />
changes in existence. "," marks the temporal divide. "-" means <br />
something ceases to exist. "*-" means all denoted entities ceases to <br />
exist. "+" means something comes into existence. <br />
<br />
'''derivation''' {*-,+} <br><br />
a -> b c ''aka fission'' <br> <br />
b c -> a ''aka fusion''<br />
<br />
'''transformation''' {,} <br><br />
a,C(a) -> a,C'(a) <br />
<br />
'''gains part''' {,} <br><br />
a,b, not has_part(a,b) -> a,b, has_part(a,b) <br />
<br />
'''loses part''' {,} <br><br />
a,b, has_part(a,b) -> a,b, not has_part(a,b) <br />
<br />
'''unification/assembly''' {,+} <br><br />
a,b -> c, has_part(c,a),has_part(c,b) <br />
<br />
'''separation/disassembly''' {-,} <br><br />
c, has_part(c,a),has_part(c,b) -> a,b<br />
<br />
Note that Barry has suggested that derivation be revised so as to not imply that the entities that exist before the temporal divide cease to exist, but retaining that a new entity is created. If this comes to be, then we might imagine a hierarchy of relations<br />
<br />
* derives_from<br />
** fused_from<br />
** fissioned_from ''yes, lousy name''<br />
** assembled_from<br />
** disassembled_from <br />
<br />
gains_part and loses_part aren't derivation since no new entity is created. In that sense they are similar to transformation.<br />
<br />
=Background Material=<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home]<br />
<br />
[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=From_BFO_to_IAO&diff=8549From BFO to IAO2009-03-20T05:08:14Z<p>Alanr: </p>
<hr />
<div>'''From Basic Formal Ontology to the Information Artifact Ontology'''<br />
<br />
July 22-23, 2009<br />
<br />
Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].<br />
<br />
Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time. <br />
<br />
Day 1:<br />
*introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative, <br />
<br />
*introduction to Referent Tracking, and its applications to the task of relating ontologies to instance data in ways useful to healthcare and biomedical research<br />
<br />
Day 2:<br />
<br />
*introduction to the Information Artifact Ontology, a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies. <br />
<br />
----<br />
'''Literature and Links'''<br />
<br />
[http://obofoundry.org OBO Foundry]<br />
<br />
[http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology]<br />
<br />
[http://org.buffalo.edu/RTU/ Referent Tracking]<br />
<br />
[http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology]<br />
----<br />
'''Faculty'''<br />
<br />
[http://org.buffalo.edu/ceusters/ Werner Ceusters] is Professor in the Psychiatry Department of the University at Buffalo (UB), Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Coordinator of Bioinformatics for the UB Health Science Faculties. <br />
<br />
[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org/ Science Commons]. His project, the Neurocommons, prototypes the use of<br />
Semantic Web technology for integrating and querying biomedical<br />
knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.<br />
<br />
[http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Boards of the Gene Ontology Consortium, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7243RO:Main Page2008-06-13T04:16:37Z<p>Alanr: </p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
Mike And Chris' Relation Ontology Proposed (MACROP), a list targets relations is [[MACROP]]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
x1 '''directly_descends_from''' x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism<br />
<br />
- x1 is an anatomical structure<br />
<br />
- x1 '''part_of''' y1<br />
<br />
- y2 is an organism<br />
<br />
- x2 is an anatomical structure<br />
<br />
- x2 '''part_of''' y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2.*<br />
<br />
'''descends_from''' is the instance level relation which is the transitive closure over '''directly_descends_from'''<br />
<br />
[* This clause still needs some work]<br />
<br />
[* On the Phenoscape project list, Jim Balhoff added the following critique of this:<br />
<br />
Something that jumps out at me in the definition of directly_descends_from:<br />
<br />
I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]<br />
<br />
A in B ''descends_from'' C in D :<br />
<br />
For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)<br />
<br />
a '''part_of''' b<br />
<br />
a '''descends_from''' c<br />
<br />
c '''part_of''' d<br />
<br />
(Note – B must be a subclade of the clade descending* from D)<br />
<br />
<br />
<br />
A1 in B1 ''homologous_to A2'' in B2<br />
<br />
iff<br />
<br />
exists A3, B3:<br />
<br />
A1 in B1 ''descends_from A3'' in B3<br />
<br />
&<br />
<br />
A2 in B2 ''descends_from'' A3 in B3<br />
<br />
(Note B1 and B2 must both be subclades of the clade descending (in the genealogical sense) from D)<br />
<br />
Note: Do we need to include time (exists & existed)? <br />
<br />
FN – just to be on the safe side we can include time – it's not obviously useful but it could block some objections and won't affect the logic.<br />
<br />
=== relation to what is in RO proposed ===<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language<br />
<br />
== Measurements ==<br />
<br />
At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation<br />
called is_measurement_of to relate a measurement to some entity. (I<br />
can't remember if these were the exact names we used).<br />
is_measurement_of is subpropertyOf is_about<br />
<br />
In the following we are discussing instance level relationships.<br />
<br />
* measurement_datum:<br />
** has_value:<br />
** in_units:<br />
** of_dimension:<br />
<br />
m1 type measurement:<br />
<br />
* m1 has_value 30^^xsd:float<br />
* m1 in_units_of degree_celsius (UO:0000027)<br />
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)<br />
<br />
(Unresolved: latter two are classes. I guess that means that<br />
in_units_of and of_dimension are annotation properties, which is a<br />
shame. Either that or degree_celsius and temperature_dimension are<br />
instances of some sort. Barry?)<br />
<br />
* room1 type site<br />
* room1 has_quality t1<br />
* t1 instance_of temperature (PATO:0000146)<br />
<br />
* m1 is_measurement_of t1<br />
<br />
It was left open exactly how to represent uncertainty in the<br />
measurement, but this was thought to be perhaps something associated<br />
with the instrument or with a collection of measurements, rather than<br />
what was associated with the individual measurement.<br />
<br />
Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMeetingNotesCompiled&diff=7198OntologyRelationsMeetingNotesCompiled2008-06-02T05:36:55Z<p>Alanr: New page: == Introductions == * Barry Smith: NCOR, OBO Foundry * Alan Ruttenberg: Science Commons, OBO Foundry * Nigam Shah: how to use relations for reasoning over biol data * Vinay Chaudhri: SR...</p>
<hr />
<div>== Introductions == <br />
<br />
* Barry Smith: NCOR, OBO Foundry<br />
* Alan Ruttenberg: Science Commons, OBO Foundry<br />
* Nigam Shah: how to use relations for reasoning over biol data<br />
* Vinay Chaudhri: SRI, knowledge building based on textbooks<br />
* David Osumi-Sutherland: FlyBase anatomy development, modeling developmental biology<br />
* Larry Hunter: building systems that represent large scale biol knowledge, current represent<br />
* Peter Midford: Phenoscape, evolutionary and spatial relationships, behavior ontologies<br />
* Melissa Haendel: anatomy and phenotype ontologies, w/ Berkeley on db querying across species<br />
* Mike Bada: bio NLP tasks and ontologies<br />
* Darren Natale: Protein Info Resource, protein ontology<br />
* Karin Verspoor: comp linguist, capturing relational info in text<br />
* Chris Mungall: phenotype/genotype representation<br />
* Wasila Dahdul: Phenoscape, anatomy curator<br />
* Mary Dolan: MGI<br />
* Fabian Neuhaus: NIST<br />
* Suzi Lewis: GO/NCBO/OBO Foundry<br />
* David Hill: ontology development and annotation<br />
<br />
== Background ==<br />
<br />
RO v.1.0 contained binary relations only. Relations are of 3 kinds: type-type (core RO relationships);<br />
type-instance; instance-instance<br />
<br />
Ontologies are representations of types (the general) and the goal of<br />
the RO is to create a limited repertoire of relations linking types to<br />
build these ontologies.<br />
<br />
For example the GO contains types only, no instances. Only something<br />
that holds for all A-s will be an assertion that holds of the type A.<br />
<br />
'All' ontologies is not ALL ontologies, there is an understanding of<br />
what the 'scope' of all is.<br />
<br />
ACTION ITEM: scope of 'all’ needs to be addressed taking into account<br />
that some ontologies (GO, FMA) are canonical, while others are not<br />
(for example, PRO includes mutant proteins)<br />
<br />
Larry: what role does time play in 'all'?<br />
<br />
Response: for process type, it plays no role, because the processes<br />
are the same regardless of time. However for continuants it does make<br />
a difference, For example, a cell membrane, isolated and experimented<br />
on, is used to draw conclusions about its role in the intact cell.<br />
<br />
The need (and goal) is for a small suite of ontologies that describe<br />
the exceptions that can be used with the reference ontologies that<br />
represent the typical/normal.<br />
<br />
=== Why keep RO small? ===<br />
<br />
Some people are going to use the relations in RO in sloppy ways. The<br />
smaller the number of options the less the possibility of misuse.<br />
More per se is not bad, but if the relations are ill defined that<br />
could be bad and would poison the well.<br />
<br />
For example, “currency has_unit $” is WRONG because there are other<br />
units of currency.<br />
<br />
Likewise, if we have “adjacent_to” then we don't need<br />
“adjacent_to_neuron/cytoplasm/organ”. There is inherently more<br />
expressivity in the class realm than in the relation realm, thus we<br />
shall pick the former vs. the latter. But there is a counter example<br />
of a useful releation from the Cell Ontology meeting: is_expressed_on_surface_of (aka EOSO)<br />
(CD4 receptor and cell type).<br />
<br />
The solution may be:<br />
<br />
* Compositional relations: could be broken down into several<br />
ontologies: RO + GO cc + cell ontology<br />
<br />
* Mix up UI with ontologies - show the mashed up relation even if it<br />
doesn't exist in the RO. That is: what is visible to the<br />
biologist/user is something interpretable/intuitive) and what goes<br />
into RO is whatever is necessary to capture as the formal, minimal<br />
relations)<br />
<br />
In other words, don't just focus on one vs. the other. Further, any<br />
proposed lists of compound relational expressions should be validated<br />
by provision of definitions in terms of RO relations.<br />
<br />
=== Spectrum of existing relations ===<br />
<br />
One end is the English side, what appears in papers and the other side<br />
are formal definitions<br />
<br />
GOAL is to find a middle ground: Larry: these should be driving the<br />
development of the minimal, formal ones. If 'expressed on surface of'<br />
can be broken down into existing core ones, then good - relational<br />
cross-products. In addition to the formal definitions, non-rigorous,<br />
intuitive definitions are also good.<br />
<br />
OPEN QUESTION: expressed_in implies located_in, what relationship does<br />
expressed_in have to existing relations in RO?<br />
<br />
Rather than creating EOSO, could also classify receptors as cell<br />
surface receptors. Describe the same biology in different ways.<br />
Instead of capturing the location in terms of the relation, capture it<br />
in the GO/CO.<br />
<br />
all-some relations<br />
<br />
All the instances of A stand in R to some B. For example: NOT -<br />
transforms_into, BUT YES - transformation_of. Or specifically, not<br />
every child transforms_into adult (single instance, apparently not on<br />
population scale), but every adult is a transformation of a child.<br />
<br />
We (RO) don't want to become Tim Berners-Lee. No some-some relations.<br />
<br />
Suzi: Are OBO_REL ids going to remain as the strings or will they<br />
transition to the numericals?<br />
<br />
ACTION ITEM: move to numerical ids<br />
<br />
Larry: Doesn't want type-type only for RO. Too constrained.<br />
<br />
Barry: type-type require instance-type definitions<br />
<br />
ACTION ITEM: Define instance level relations as well. Clarity is<br />
important. Relations need to be clarified whether they be used for<br />
type_type/type_instance/instance_instance.<br />
<br />
Well-defined relationships are the ideal; clear to us, easy to explain<br />
to others<br />
<br />
Chris: Should we split out part_of for instances from part_of for types? How would we do this?<br />
# Drop type-level relations (DON"T LIKE THIS)<br />
# Separate ids for instance and class level relations, different namespaces (THIS IS THE CHOICE, details not important right now)<br />
# Clarify current 'punning' semantics, same id, means different thing in different contexts (however, sometimes it's hard to tell what the context is)<br />
# not all type level relations can be defined in terms of instance level relations, need to work on both fronts<br />
<br />
Long term proposal: Provide CommonLogic definition, port this to obo<br />
and owl as necessary - Fabian has some basic work done, Alan can help<br />
in translation but doesn't want to be the blocker. Have this in place<br />
for the next release.<br />
<br />
Are ternary relationships possible? Yes.<br />
<br />
Cyc solution (SRI): Rule macro predicates: Relation 'all' exists.<br />
Has_part A, B.<br />
<br />
BFO (Basic Formal Ontology) is an upper ontology of entities, and the<br />
RO is an upper ontology of relations. The ro_bfo_bridge has domain and<br />
range constraints<br />
<br />
e.g. id OBO_REL:has participant; the domain is span: Occurrent, and<br />
the Range is snap:Continuant<br />
<br />
This is good in that they are separate and independent, but it is very<br />
awkward to maintain, BFO is primarily realized in owl, RO is in<br />
obo. The solution is to use a common language<br />
<br />
ACTION ITEM: RO should have a commitment to an upper ontology and it<br />
shall be BFO.<br />
<br />
RO tracker is located at http://sourceforge.net/tracker/?group_id=76834&atid=947684. Requests can be<br />
requirements-oriented. E.g. I need a relation for this purpose, please<br />
help me formalize it.<br />
<br />
One solution to has_part: add the qualifiers into it: all_has_part,<br />
for example<br />
<br />
== Representing Developmental Anatomy ==<br />
<br />
Presenter: David Osumi-Sutherland<br />
<br />
Current limitations: RO can't specify timing of transitions, can't use<br />
existing part_of relations to apply to 'sometimes'. What is needed is<br />
a system for capturing stage specific part relations.<br />
<br />
What is developmental time?<br />
<br />
In a developmental process, many events happen in an invariant order,<br />
these events can be used as markers of developmental progress or time<br />
(standard stage series). E.g. gastrulation is a process, which can be<br />
arbitrarily divided into stages based on marker events<br />
<br />
Stage = BFO, fiat part of process. In other words marker events:<br />
birth, death, transformation of an anatomical structure/ beginning,<br />
end, a key point in a developmental process<br />
<br />
Timing relationships: before, simultaneous which can both be derived<br />
from before_or_simultaneous_with<br />
<br />
(Werner joins discussion at 11:05 am local time, during David's example of Drosophila oogenesis)<br />
<br />
Question is: How to deal with relative processes? That is, X happens<br />
during Y only during process Z?<br />
<br />
Ternary relations? A before B during C? - but these are not supported<br />
in OWL, so have to use binary relations.<br />
<br />
Solution: for each type for which timing is to be captured, record a<br />
reference occurrent (see slides for rest of detail). E.g. gastrulation<br />
reference_occurrent embryogenesis. There is still an issue with<br />
individual somite geneses - generalize to somitogenesis? (recurrent<br />
process) - individual timing relationships<br />
<br />
ACTION ITEM: Add new timing relationships: begins_at_end_of,<br />
begins_during, ends_during, begins_before, ends_after,<br />
simultaneous_with, happens_during<br />
<br />
In the future we hope to use ternary relationships. The solution for<br />
right now (that will work with the existing tools) is to use binary<br />
that can be mapped to ternary ones in the future. But David (and<br />
others) wants to reason using these relationships NOW. Argument for<br />
ternary relationship: can have multiple reference processes. <br />
<br />
Larry's example: oocyte maturation, follicle maturation with regards<br />
to oogenesis and with regards to life of the organism.<br />
<br />
(From Larry)<br />
<br />
Here is my example of why a single reference occurrence doesn't work<br />
(and we need a ternary relation in order to capture the reference<br />
occurrent for a particular temporal relation):<br />
<br />
* Oocyte fate determination <before> oocyte maturation [reference occurrent oogenesis]<br />
* oocyte maturation <before> follicle maturation [reference occurrent lifespan]<br />
<br />
First, note that oocyte maturation needs to have both reference<br />
occurrents in order to be able to assert these two things. These are<br />
different in that there are a bunch of oogenesis occurents (so we need<br />
the reference occurrent), but they all end before the first follicle<br />
maturation (so we need the other reference occurrent). Incidentally,<br />
we should be able to infer Oocyte fate determination <before> follicle<br />
maturation on something like the basis that oogenesis <part-of><br />
lifespan.<br />
<br />
ACTION ITEM: fix phrasing to timing relationships (first_exists_during<br />
vs. begin_to_exist) to be consistent.<br />
<br />
Fabian demonstrated an example of a reasoner that uses David/Fabian's<br />
new temporal relations. Reasoning at instance level breaks, is too<br />
slow, but reasoning at type level works.<br />
<br />
Define: what is the same and what is new? E.g. Neuroblast vs. neuron<br />
<br />
Alan: does NOT like succeeds, doesn't like the generalization, either<br />
have specifics or general, not both.<br />
<br />
LUNCH BREAK occurred as a way to interrupt the escalating discussion/argument.<br />
<br />
== derives_from vs. transformation_of == <br />
<br />
Presenter: Melissa Haendel<br />
<br />
Gave specific examples of develops_from and why this needs to be<br />
transitive: heart development. But the problem is that this is not the<br />
definition of develops_from. Do we care about identity? If not, get<br />
rid of transformation_of and keep develops_from.<br />
<br />
develops_from<br />
--derives_from<br />
--transformation_of<br />
<br />
Darren example: A -> A-PO4, is this transformation or derivation?<br />
<br />
Define identity function first, then can decide what is transformation<br />
and what is not. Views on what identity is, is the hard part -<br />
complicated, context-dependent. For example, consider:<br />
<br />
A -> B -> C -> D -> E<br />
<br />
Where B derives from A, C transformation of B, C derives from D, and E buds from D<br />
<br />
What is the relation of A to E? Is it develops from, needed from<br />
transitive closure, good for querying<br />
<br />
Alan's issue: if there's any lack of clarity of when to use<br />
derives_from vs. transformation_of, then the system breaks down<br />
<br />
SOLVE THE IDENTITY PROBLEM!!!!! (and solve it now)<br />
<br />
Cell division and budding are pretty clear: division: A -> B + C<br />
whereas budding: A -> A + B<br />
<br />
What are the examples that are clearly transformation? Rule is to stay<br />
at same level of granularity, anatomical parts down to the cellular<br />
level (NOT molecular level) - id1 => id1<br />
<br />
* caterpillar -> pupa -> butterfly<br />
* neural plate transformation of neural tube<br />
* neuron -> mature neuron<br />
* mature leaf -> senescent leaf<br />
* What are the examples that are clearly derives from? id1 => id2<br />
* [mandible derives from cranial neural crest] - a bit controversial because of the 'scaffolding' involved in bone formation<br />
* U2 neuron derives from GMC71B<br />
* leaf primordium derives from shoot apical meristem<br />
* neural crest derives from neural tube<br />
<br />
Alan: Is identity reality or perspective?<br />
<br />
If develops_from is used in cases where we don't know what to say ------ leads to a lazy way of usage. <br />
<br />
Biologists: we KNOW it's develops from, we don't know whether it's<br />
derives from or transformation of. A process needs to have a beginning<br />
and the end, The thing that develops does not have to be there at the<br />
beginning of the process but it needs to be there at some point during<br />
the process<br />
<br />
ACTION ITEM: make a biological definition of develops_from, test at<br />
all levels of granularity, provide cases of NOT develops_from Is<br />
transformation maturation? Is that the key? Not the single<br />
criterion. Definitely not at the RNA level. Maybe just at the<br />
organismal level. Can one have maturation independent of some<br />
process? No.<br />
<br />
COFFEE BREAK<br />
<br />
== Spatial Relations, Coming From Rcc8 ==<br />
<br />
* disconnected<br />
* externally connected - adjacent?<br />
* equal<br />
* partially overlapping<br />
* tangential proper part - contained in and adjacent to<br />
* tangential proper part inverse<br />
* non-tangential proper part<br />
* non-tangential proper part inverse<br />
<br />
Don't want to make projections of 3D onto 2D.<br />
<br />
If we want to use RCC keep the dimensions the same at the instance<br />
level. We should look at geospatial ontologies/descriptions for car<br />
(?) part manufacturing?<br />
<br />
What is the difference between R and R' where: “town R county” and<br />
“island R' lake”? Or for a biological example: urine R bladder<br />
(contains? located?)<br />
<br />
ACTION ITEM: have v. small meeting with spatial ontology (CAD,<br />
connectivity, etc.) experts + some biologists to adapt existing<br />
spatial relations to RO, who to invite? Tony Cohn. Thomas<br />
Bittner. Karen Pittman, Cycorp. Xenia Fiorentini, NIST. GOAL of this<br />
meeting: get spatial relations into RO<br />
<br />
=== Spatial use cases ===<br />
Presenter: Wasila Dahdul<br />
<br />
teeth R bone: What is this? attached_to? connected_to? When would you use one over the other?<br />
<br />
bona fide boundary vs. fiat boundary Does it matter? When does it<br />
matter? It is sufficient to share a boundary? Does it have to be a<br />
bona fide boundary? Connected_to is currently a fiat boundary as in<br />
the FMA: x is connected to y if X and y share a fiat (somewhat<br />
arbitrary) boundary (doesn't reflect any physical discontinuity)<br />
<br />
Vinay: connectedness: A is connected to B means that B will move if A<br />
moves. It is grounded in physical actions/movement<br />
<br />
Attached_to is a connected relationship where there is a large<br />
disparity between the size of the two objects. E.g. muscle attached_to<br />
bone, tooth attached_to bone, arm attached_to body, NOT body<br />
attached_to arm,<br />
<br />
In the case of ball and socket joint they are connected via fluid. The<br />
thought experiment is whether there are more kinds of 'connected' for<br />
things, force exerted, force connectedness? fiat connectedness?<br />
<br />
Fabian: what kind of reasoning do you want to get out of this/support<br />
with these relationship types? Both approaches have their merits.<br />
What is the purpose? What would be useful?<br />
<br />
He suggests, just have a single relationship called 'connected' which<br />
covers both.<br />
<br />
Barry's motion: add attachment, connected, synaptic connection, get<br />
definitions from FMA which need improvement, improve them, submit to<br />
biologists for review with examples, find out why FMA used them that<br />
way. It looks like discussions on the RO list led to use of these<br />
proposed types (with same names) in the opposite direction. Is there<br />
really confusion or not? Not.<br />
<br />
=== Overlaps relationship ===<br />
<br />
Peter Midford<br />
<br />
Overlaps means two things share parts, for example: synovial joint <br />
* A part of Bone 1<br />
* A part_of Synovial Joint 1<br />
* Therefore Bone 1 overlaps Synovial Joint 1<br />
<br />
Logically, everything overlaps with its parts. Are these symmetric on<br />
the instance level but not on the type level? This seems the case for<br />
the joint example. However uterine tract overlaps urogenital system<br />
but NOT urogenital system overlaps uterine tracts<br />
<br />
ACTION ITEM: Add symmetric_overlaps/mutally_overlaps, modify the<br />
proposed definition.<br />
<br />
If the femur overlaps knee joint then the reverse is knee joint<br />
overlaps femur. Are both true? Is it important to capture that this<br />
is a symmetric overlap?<br />
<br />
Wasila notes that in the spatial ontology top level contains both<br />
dependent and independent continuants: anatomical axis, anatomical<br />
axis direction, anatomical compartment, anatomical compartment<br />
boundary, anatomical gradient, anatomical region - included margins,<br />
anatomical section, anatomical surface<br />
<br />
=== Character, Character State ===<br />
What is a character description? Characters from a phylogenetic<br />
perspective, cover the variation in a single bone, how is it shaped<br />
differently across different species. Sample character: shape of<br />
posterior margin of lateral ethmoid has one phenotype in one species<br />
and another phenotype in another species. Of another example: the<br />
Character is the presence or absence of bone X. Or the position of<br />
bone X with regard to bone Y, where bone X may be posterior to Bone Y<br />
or Bone X may be anterior to Bone Y.<br />
<br />
* ACTION ITEM: make GO spatial-related process definitions consistent with spatial ontology<br />
* ACTION ITEM: add more axis-related terms to spatial list (adaxial/abaxial, apical/basical, caudal-cephalic)<br />
* ACTION ITEM: take anything relational out of Spatial and move to RO, check out whether 'vicinity of' needs to stay<br />
* ACTION ITEM: remove spatial stuff from FMA<br />
* ACTION ITEM: decide what needs to stay in PATO and what needs to go into RO - punt to tomorrow<br />
* ACTION ITEM: Define distal and proximal, ternary relationships?<br />
* ACTION ITEM: Add medial and lateral? <br />
<br />
== Agency == <br />
<br />
Chris: is_agent.<br />
<br />
Is there really agency ? NO because of the absence of intent. But<br />
still need something more specific than has_participant, e.g. heart<br />
process has_participant heart<br />
<br />
Alan : NO NEED FOR AGENT! (see his very complicated slide about how<br />
one can get around this using roles and owl). The only role related<br />
relation Alan thinks is necessary: realization_of<br />
<br />
Fabian: participates in?<br />
<br />
Is it one or is it a bunch? punt to tomorrow<br />
<br />
== Regulates ==<br />
<br />
David Hill<br />
<br />
Fabian: can processes that regulate a process be a part of that process? Yes. Good.<br />
<br />
Ignoring regulations of qualities for now? Yes. There are not targets in the GO that already exist.<br />
<br />
Alan: so many things affect transcription, how do you distinguish some that regulate and some that don't<br />
<br />
By restricting to occurrents, we avoid problems that could arise from<br />
things like 'temperature' and 'nucleotide concentration' affecting the<br />
'rate, frequency, extent.' I.e. RNA pol II does not regulate<br />
transcription, it carries out transcription.<br />
<br />
What about other parts of the transcription machinery? If they're<br />
always there, they do transcription. If they're sometimes there, they<br />
are regulating.<br />
<br />
If it's static canonically, it does not regulate.<br />
<br />
Alan has problems with the current definition: one that includes all<br />
the things based on your intuition. cite the right entities. We<br />
should have some procedure so that I can take two processes that are<br />
happening in the vicinity of the other process that let's me tell<br />
whether one is regulatory and the other is not. Right now, it's not<br />
workable. Define rate. Who are the participants? What is the rate<br />
of a process? Duration makes sense. What is frequency of a process?<br />
His sense is that the current definition is completely lexically<br />
driven. Define in terms of a continuant which feeds into the process<br />
(did I catch this right?). In as many processes as possible.<br />
<br />
There are participants in the BMP signaling pathway that directly do<br />
the regulation of transcription. There are proximate processes that<br />
affect transcription.<br />
<br />
Suzi: it's the other way around. There is big effort in GO to use<br />
regular syntax when naming things. These things got named this<br />
because of what they did.<br />
<br />
You can't change a canonically static process<br />
<br />
The rate of a process is how many times does this get initiated?<br />
<br />
Larry: Can Alan improve 'regulates' any further?<br />
<br />
Qualities of occurrents? Can they exist? <br />
<br />
Causation - regulation - How far back do you go? What is the scope?<br />
Basic metabolic processes regulated EVERYTHING. Where is the<br />
beginning and end? What is direct and indirect?<br />
<br />
possible solution: use comparatives, why this instead of that? The<br />
comparative approach helps us do science. All of experimentation is<br />
comparative.<br />
<br />
Why isn't the production of BMP part of this process? Probably yes,<br />
but this figure was taken out of a paper.<br />
<br />
Is regulates transitive? If A regulates B and B regulates C, does A regulate C?<br />
<br />
ACTION ITEM: improve on the current 'regulates' definition referring<br />
to continuants which interact and fulfill their functions, then see if<br />
this definition works and can be applied to the use case/s that we<br />
have<br />
<br />
When known, the most proximal step to a process, should be the<br />
regulator of that process. In the example, binding of SMAD4 complex<br />
regulates transcription, all the previous stuff regulates<br />
transcription by inference.<br />
<br />
Do we need 'regulates' AND 'indirectly_regulates'? Not really.<br />
<br />
Is regulation a mix of instructive and permissive signals?<br />
<br />
Hh signaling regulates limb development? Melissa/David: yes David OS:<br />
BS! -lots of argument, David H changes his mind, Hh signalling part<br />
of limb development. In summary, instructive signals would be part of<br />
the process<br />
<br />
BMP signaling is required for dorsal/ventral patterning, it is<br />
instructive, it needs to be a part of.<br />
<br />
Darren: If all we know that BMP binding the receptor results in change<br />
in tsc, then create BMP signaling pathway regulates transcription. As<br />
we know more, add more information to the ontology, change the<br />
annotation to something more specific.<br />
<br />
Larry: why take away the more general and only keep the detail?<br />
<br />
How many senses of 'regulates' are being lumped together in the<br />
relationship 'regulates'?<br />
<br />
END DAY ONE - GOING TO DINNER at 6:20 pm after beginning at 8:50 am<br />
<br />
Day 2: starting at 9:13 am with tasks from last night<br />
<br />
== Develops_from homework ==<br />
<br />
Biologist, logicians to try to come up with definitions of<br />
develops_from, discuss need for transformation_of, derives_from.<br />
<br />
=== Biological ===<br />
<br />
Melissa/David: Biological definition of develops_from (at the cellular level) and the continuity of cell lineage.<br />
<br />
Darren: c develops from d iff there is a continuity of lineage extending from d to c, where:<br />
# the existence of d preceds the existence of C<br />
# some portion of the material of d is retained in the material of c<br />
# one can trace the event or set of events linking d to c<br />
<br />
What is 'material'? <br />
<br />
Alan: still need and should have developmental specific definition,<br />
build the specific definitions (developmental, protein) first, then<br />
build the general one later<br />
<br />
* cell1 parent_of cell 2 (single division process occurs)<br />
* cell1 in_lineage_with cell2, if cell1 = cell2 or cell2 is some sequence of parent relationships to the cell2 <br />
<br />
(develops_from within a single organism) - gets around Larry's lung<br />
developed from his grandmother's ovary<br />
<br />
anatomical structure 1 develops from anatomical structure 2 iff some<br />
cell in anatomical structure 2 in lineage with some cell in anatomical<br />
structure 1.<br />
<br />
Is there a problem with immaterial entities? Eg. blastocoel. Not<br />
really, we don't care about them. What about secretions, things that<br />
are built out of secreted structures? How do we extend to those? Use<br />
'secretes'?)<br />
<br />
This basic definition appears to apply on multiple levels: cellular,<br />
biochemical, anatomical structures and organisms. We will try this<br />
out.<br />
<br />
Suzi: some events that result in something new, some events that<br />
result in 'rearrangement of material'<br />
<br />
Alan: we want at least the cell biological level defined, good logical<br />
definition in the terms that biologists use and understand, build from<br />
the cellular level up.<br />
<br />
=== Logical ===<br />
<br />
(2) ontologist's justification of why the two children terms are important ;<br />
<br />
Biologists don't care explicitly, use it implicitly. Ignore the two children for now.<br />
<br />
== Homology ==<br />
<br />
Melissa: homology relation? 'descends_from'<br />
homologous structures vs. analogous structures. For example, mouse limb homologous to human limb, but bird wing is analogous to bat wing<br />
character = quality (shape of bone margin)<br />
character state = variability in quality<br />
Peter:<br />
Review of tree building based on three characters, looking at the various character states independently reveals different things about the individual ancestral states. Comparing two trees derived from two different sets of characters reveals different phylogenetic relationships. <br />
Homology evidence codes: (in use by Phenoscape using Phenote)<br />
* inferred from morphological similarity<br />
* inferred from positional similarity<br />
* inferred from developmental similarity<br />
* inferred from compositional similarity<br />
* inferred from gene expression similarity<br />
* inferred from phylogeny<br />
<br />
Definition: (see RO meeting wiki but remove taxon reference and replace by 'population', remove the Instance 3-ary relation - Melissa editing now)<br />
<br />
directly_descends_from = (definition, get rid of partially a copy, get rid of determination is instance_level<br />
<br />
descends_from = ? in_lineage_with from the earlier discussion on develops_from<br />
<br />
This looks good to Barry, fix italicization issue with definition<br />
<br />
common ancestor forelimb<br />
/ \<br />
/ \ descends_from<br />
/ \<br />
/ \<br />
bat wing human arm <br />
bat wing <-homologous_to -> human arm<br />
<br />
ACTION ITEM: Two relations: 'descends_from' (not the final string),<br />
homologous_to both with definitions - generalize definition, work on<br />
last bit of definition relating to genetic material and genetic<br />
programs<br />
<br />
What do you use to describe the relationship between a parent<br />
anatomical structure and a child anatomical structure<br />
<br />
Darren: current definition is restricted to anatomical structures,<br />
huge problem for proteins/genes<br />
<br />
Chris: structure of definition is fine, need to generalize homology to<br />
apply to proteins/genes, anatomical structure could broadly refer to<br />
character states<br />
<br />
Melissa: need homologous_to NOW for anatomical structures<br />
<br />
Note: Just because two anatomical structures are homologous, it does<br />
not mean that its parts are homologous. Structures that are<br />
homologous could use completely different programs.<br />
<br />
David OS: transitive closure is important only between two 'generations'<br />
* 1001<br />
* 0001<br />
* 0101<br />
* 0110<br />
* 0100<br />
<br />
David OS: evolved_from relationship. The homologous_to relationship<br />
does not involve time, can hold between simultaneously existing<br />
entities: human arm and bat wing. In contrast, evolves_from does<br />
involve time: human arm and 'ancestral forelimb'<br />
<br />
Is evolves_from built from directly_descends_from? Yes. Figure out<br />
strings to make them parallel.<br />
<br />
BREAKTIME<br />
<br />
Regulates discussion: not reopened to avoid non-constructive and never<br />
ending discussion. <br />
<br />
Action Item: David, Tanya and Chris will come up with a more rigorous<br />
definition of 'regulates' and present that to the group for review.<br />
<br />
== Epistemic relations or how do we know what we know? ==<br />
Presenter: Larry Hunter<br />
<br />
* supports<br />
* is_supported_by (inverse)<br />
* contradicts<br />
* is_contradicted_by (inverse)<br />
<br />
What is scientific evidence? (evidence that supports a hypothesis - 'citeable'?)<br />
* peer review<br />
* capable of being communicated<br />
* secret information can't be scientific evidence<br />
<br />
Making physical objects scientific evidence is a problem???<br />
* "bug" with pins in it? scientific specimen: is this evidence?<br />
* how about clones? <br />
<br />
information entity - something that is communicated<br />
<br />
GO gene_association file (GAF) use case<br />
<br />
3 epistemic columns: <br />
<br />
* DB:reference: <assertion> is_supported_by <DB:reference><br />
* NOT qualifier - flips evidence, not assertion: <assertion> is_contradicted_by <DB:reference><br />
* evidence code<br />
<br />
How to handle one piece of evidence that supports two (or more) assertions in different ways.<br />
I.e. sentence 1 provides info for IDA and IC, how do we capture these multiple roles?<br />
# sub-relations: subclass binary supports, e.g. supports_by_direct_assay<br />
# ternary relations: Make supports a ternary relation: supports <assertion> <evidence> <evidence type><br />
# PMID = ECO type <br />
# represent the inference<br />
<br />
<pre><br />
inference type<br />
^<br />
/ (solid line)<br />
/<br />
supports /<br />
asserted sentence <--------------inference (process used to arrive at assertion)<br />
<br />
^ /<br />
| /<br />
| (both dotted) / <br />
| /<br />
| / <br />
| V<br />
PMID<br />
</pre><br />
<br />
* asserted sentences have a speaker<br />
* asserted sentences = things we believe are true<br />
* (When all fails, speak louder and/or faster.)<br />
* partial constraints for supports?<br />
* Barry: add to ROIL<br />
<br />
== TAIR Relations ==<br />
<br />
Tanya: has(function)<br />
<br />
ACTION ITEM: table: map relationship_types to RO relations if known,<br />
if not put?, also add range of things that go into term2, send to<br />
group (obo-discuss, ro). For protein modification, use psi-mod<br />
(potential target for)<br />
<br />
== Biochemical relations ==<br />
<br />
Presenter: Mike Bada<br />
<br />
Built GO to CheBI cross products<br />
<br />
Functions defined in terms of processes by which they can be realized:<br />
<br />
kinase function = catalytic function THAT is_realized_in GO:kinase activity<br />
<br />
Definitions are wrong!<br />
<br />
THEY WANT: Catalytic processes and Catalytic activities defined in<br />
terms of processes they are catalyzing:<br />
<br />
GO:kinase activity = GO:molecular_function THAT results_in_catalysis_of GO:phosphorylation<br />
<br />
This (Mike thinks) necessitates an ontology of types of (bio)chemical<br />
reactions. GO lays out potential to do something vs. the doing<br />
something. These both exist. We will not instantiate BOTH function<br />
AND functioning. It is simpler to make links between functions and<br />
processes.<br />
<br />
Process(function) = realization of function, and Function (process) = realized_as process<br />
<br />
Alan: automatic generation of one term when the other is made<br />
<br />
DavidH: how about creating links between MF and BP and the relationship describes that link?<br />
<br />
Discussion about Mike's definitions and how they could be improved.<br />
<br />
David H: We will create a relationship describing that a gene product<br />
has the potential to execute a molecular function (has disposition to<br />
realize?). This way the MF ontology describes the realization<br />
(execution) of a molecular function. These executions will then be<br />
allowed to be part_of BPs. All MFs are part_of some type of BP.<br />
<br />
=== TMRs, cross-products ===<br />
<br />
ACTION ITEM: Larry will create and use too many relations (TMRs) Mike<br />
has made now as 'macros' or shortcuts while the RO people write the<br />
underlying framework that will support them. If some of them don't<br />
break down properly, these will be fixed. Relations will be sent to<br />
Alan together with Mike for training. Code named: Mike And Chris<br />
Relations Ontology, or ROC, ROIL, MAC-RO, MAC-ROP<br />
<br />
Chris: cross products, GO biological process and cell ontology<br />
<br />
There are a bunch of different proposed relations: see ro_proposed:<br />
aka Chris' macros (how many? 12, development, anatomy and cell, for<br />
chemicals about 10)<br />
<br />
ACTION ITEM: find an example of Chris' macro where there are two<br />
relations that identify two participants to verify claim - source and<br />
destination for a transport event<br />
<br />
ACTION ITEM: again, find a way to translate the macros into a formal definition<br />
<br />
Pattern: x results in A x2; A is term from another ontology<br />
<br />
Alternate: for some y A(y); participant (x2,y) ^<br />
<br />
(tried to transcribe the above from Fabian's writing on the board but missed some parts)<br />
<br />
Necessary is easy, necessary and sufficient is hard<br />
<br />
== Summary of Action Items == <br />
<br />
# Scope of 'all’ needs to be addressed taking into account that some ontologies (GO, FMA) are canonical, while others are not (for example, PRO includes mutant proteins)<br />
# Move to numerical ids<br />
# Define instance level relations as well. Clarity is important. Relations need to be clarified whether they be used for type_type/type_instance/instance_instance.<br />
# RO should have a commitment to an upper ontology and it shall be BFO.<br />
# Add new timing relationships: begins_at_end_of, begins_during, ends_during, begins_before, ends_after, simultaneous_with, happens_during<br />
# Stages and temporal relations: are there cases where we do not need the reference process?<br />
# Fix phrasing to timing relationships (first_exists_during vs. begin_to_exist) to be consistent.<br />
# Make a biological definition of develops_from, test at all levels of granularity, provide cases of NOT develops_from<br />
# Have v. small meeting with spatial ontology (CAD, connectivity, etc.) experts + some biologists to adapt existing spatial relations to RO, who to invite? Tony Cohn. Thomas Bittner. Karen Pittman, Cycorp. Xenia Fiorentini, NIST. GOAL of this meeting: get spatial relations into RO<br />
# Spatial relations: add to ro attachment, connected, synaptic (use fma definitions, work on them, circulate to biologists to vet)<br />
# Add symmetric_overlaps/mutally_overlaps, modify the proposed definition.<br />
# Make GO spatial-related process definitions consistent with spatial ontology. Fix, harmonize, extract from appropriate places -- anything relational from spatial.obo to ro<br />
# Add more axis-related terms to spatial list (adaxial/abaxial, apical/basical, caudal-cephalic). Make precise what is meant by medial, lateral -- dorsal, ventral -- proximal, distal -- anterior, posterior<br />
# Take anything relational out of Spatial and move to RO, check out whether 'vicinity of' needs to stay<br />
# Remove spatial stuff from FMA<br />
# Decide what needs to stay in PATO and what needs to go into RO - punt to tomorrow<br />
# Define distal and proximal, ternary relationships?<br />
# Add medial and lateral? <br />
# Improve on the current 'regulates' definition referring to continuants which interact and fulfill their functions, then see if this definition works and can be applied to the use case/s that we have<br />
# Two relations: 'descends_from' (not the final string), homologous_to both with definitions - generalize definition, work on last bit of definition relating to genetic material and genetic programs. new relations descends_from (already used so need a different string!), homologous_to can be inferred.<br />
# Evidence: add supports and contradicts relationships, small working group for domain and range<br />
# David, Tanya and Chris will come up with a more rigorous definition of 'regulates' and present that to the group for review.<br />
# Table: map relationship_types to RO relations if known, if not put? Also add range of things that go into term2, send to group (obo-discuss, ro). For protein modification, use psi-mod (potential target for)<br />
# Tair: make table of tair relations, column for ro term if it exists, send to ro group make request for needed terms<br />
# Larry will create and use too many relations (TMRs) Mike has made now as 'macros' or shortcuts while the RO people write the underlying framework that will support them. If some of them don't break down properly, these will be fixed. Relations will be sent to Alan together with Mike for training. Code named: Mike And Chris Relations Ontology, or ROC, ROIL, MAC-RO, MAC-ROP<br />
# Find an example of Chris' macro where there are two relations that identify two participants to verify claim - source and destination for a transport event<br />
# Again, find a way to translate the macros into a formal definition</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7197OntologyRelations2008-06-02T05:01:35Z<p>Alanr: /* Minutes, Notes and Presentation */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Minutes, Notes and Presentation ==<br />
* [[Media:May 2008 RO meeting minutes.doc]]<br />
* [[OntologyRelationsMay19MeetingNotes]]<br />
* [[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
* [[Media:regulates.ppt]]<br />
* [[Media:overlaps.ppt]]<br />
* [[Media:RO-denver-cjm.ppt]]<br />
* [[Media:dahdul-ROmeeting.ppt]]<br />
* [[Media:Fabian developmental relations.pdf]]<br />
* [[Media:Fabian develops_from.pdf]]<br />
* [[Media:melissa development examples.ppt]]<br />
* [[Media:Homology.ppt]]<br />
* [[Media:Hunter Epistemic relations.ppt]]<br />
* [[Media:Ruttenberg-ro.pdf]]<br />
<br />
* [[OntologyRelationsMeetingNotesCompiled]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7193OntologyRelationsMay19MeetingNotes2008-06-01T04:48:49Z<p>Alanr: Add Larry's example</p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.<br />
<br />
Same or different identifiers for class/instance relations such as part_of?<br />
<br />
Numeric ids for RO terms?<br />
<br />
RO commits to BFO as upper level ontology<br />
<br />
RO will have separate identifiers for class level and instance level relations. (And different class level ids where the quantification is different). <br />
<br />
We will use numerical ids for RO terms.<br />
<br />
Development relations: Questions about "simple" binary versions, versus refoccurent (one per occurrent) versus ternary (more than one refoccurrent)<br />
<br />
AI: Larry write up oocyte maturation/follicle generation case motivating more than one refoccurent<br />
<br />
AI: Fabian to write up case: begins_to_exist_during 9, ends_existence_during 11. Query: Does it exist during 10?<br />
<br />
AI: Barry to offer new and consistent names for the development temporal relations<br />
<br />
AI: Organize meeting with spatial relation experts to extend RO<br />
<br />
== Larry Hunter's example of why a single reference occurrence doesn't work ==<br />
<br />
Here is my example of why a single reference occurrence doesn't work (and we need a ternary relation in order to capture the reference occurrent for a particular temporal relation):<br />
<br />
* Oocyte fate determination <before> oocyte maturation [reference occurrent oogenesis]<br />
* oocyte maturation <before> follicle maturation [reference occurrent lifespan]<br />
<br />
First, note that oocyte maturation needs to have both reference occurrents in order to be able to assert these two things. These are different in that there are a bunch of oogenesis occurents (so we need the reference occurrent), but they all end before the first follicle maturation (so we need the other reference occurrent).<br />
<br />
Incidentally, we should be able to infer Oocyte fate determination <before> follicle maturation on something like the basis that oogenesis <part-of> lifespan.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7163OntologyRelations2008-05-23T07:19:00Z<p>Alanr: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Notes and Presentation == <br />
* [[OntologyRelationsMay19MeetingNotes]]<br />
* [[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
* [[Media:regulates.ppt]]<br />
* [[Media:overlaps.ppt]]<br />
* [[Media:RO-denver-cjm.ppt]]<br />
* [[Media:dahdul-ROmeeting.ppt]]<br />
* [[Media:Fabian developmental relations.pdf]]<br />
* [[Media:Fabian develops_from.pdf]]<br />
* [[Media:melissa development examples.ppt]]<br />
* [[Media:Homology.ppt]]<br />
* [[Media:Hunter Epistemic relations.ppt]]<br />
* [[Media:Ruttenberg-ro.pdf]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7162OntologyRelations2008-05-23T07:18:40Z<p>Alanr: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
Notes and Presentations:<br />
* [[OntologyRelationsMay19MeetingNotes]]<br />
* [[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
* [[Media:regulates.ppt]]<br />
* [[Media:overlaps.ppt]]<br />
* [[Media:RO-denver-cjm.ppt]]<br />
* [[Media:dahdul-ROmeeting.ppt]]<br />
* [[Media:Fabian developmental relations.pdf]]<br />
* [[Media:Fabian develops_from.pdf]]<br />
* [[Media:melissa development examples.ppt]]<br />
* [[Media:Homology.ppt]]<br />
* [[Media:Hunter Epistemic relations.ppt]]<br />
* [[Media:Ruttenberg-ro.pdf]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=File:Ruttenberg-ro.pdf&diff=7161File:Ruttenberg-ro.pdf2008-05-23T07:16:01Z<p>Alanr: </p>
<hr />
<div></div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7160OntologyRelations2008-05-23T07:13:25Z<p>Alanr: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Media:Fabian developmental relations.pdf]]<br />
<br />
[[Media:Fabian develops_from.pdf]]<br />
<br />
[[Media:melissa development examples.ppt]]<br />
<br />
[[Media:Homology.ppt]]<br />
<br />
[[Image:Hunter Epistemic relations.ppt]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7083OntologyRelationsMay19MeetingNotes2008-05-19T21:13:04Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.<br />
<br />
Same or different identifiers for class/instance relations such as part_of?<br />
<br />
Numeric ids for RO terms?<br />
<br />
RO commits to BFO as upper level ontology<br />
<br />
RO will have separate identifiers for class level and instance level relations. (And different class level ids where the quantification is different). <br />
<br />
We will use numerical ids for RO terms.<br />
<br />
Development relations: Questions about "simple" binary versions, versus refoccurent (one per occurrent) versus ternary (more than one refoccurrent)<br />
<br />
AI: Larry write up oocyte maturation/follicle generation case motivating more than one refoccurent<br />
<br />
AI: Fabian to write up case: begins_to_exist_during 9, ends_existence_during 11. Query: Does it exist during 10?<br />
<br />
AI: Barry to offer new and consistent names for the development temporal relations<br />
<br />
AI: Organize meeting with spatial relation experts to extend RO</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7066OntologyRelationsMay19MeetingNotes2008-05-19T17:53:04Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.<br />
<br />
Same or different identifiers for class/instance relations such as part_of?<br />
<br />
Numeric ids for RO terms?<br />
<br />
RO commits to BFO as upper level ontology<br />
<br />
RO will have separate identifiers for class level and instance level relations. (And different class level ids where the quantification is different). <br />
<br />
We will use numerical ids for RO terms.<br />
<br />
Development relations: Questions about "simple" binary versions, versus refoccurent (one per occurrent) versus ternary (more than one refoccurrent)<br />
<br />
AI: Larry write up oocyte maturation/follicle generation case motivating more than one refoccurent<br />
<br />
AI: Fabian to write up case: begins_to_exist_during 9, ends_existence_during 11. Query: Does it exist during 10?<br />
<br />
AI: Barry to offer new and consistent names for the development temporal relations</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7065OntologyRelationsMay19MeetingNotes2008-05-19T17:43:20Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.<br />
<br />
Same or different identifiers for class/instance relations such as part_of?<br />
<br />
Numeric ids for RO terms?<br />
<br />
RO commits to BFO as upper level ontology<br />
<br />
RO will have separate identifiers for class level and instance level relations. (And different class level ids where the quantification is different). <br />
<br />
We will use numerical ids for RO terms.<br />
<br />
Development relations: Questions about "simple" binary versions, versus refoccurent (one per occurrent) versus ternary (more than one refoccurrent)<br />
<br />
AI: Larry write up oocyte maturation/follicle generation case motivating more than one refoccurent</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7064OntologyRelationsMay19MeetingNotes2008-05-19T17:37:07Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.<br />
<br />
Same or different identifiers for class/instance relations such as part_of?<br />
<br />
Numeric ids for RO terms?<br />
<br />
RO commits to BFO as upper level ontology<br />
<br />
RO will have separate identifiers for class level and instance level relations. (And different class level ids where the quantification is different). <br />
<br />
We will use numerical ids for RO terms.<br />
<br />
Development relations: Questions about "simple" binary versions, versus refoccurent (one per occurrent) versus ternary (more than one refoccurrent)</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7057OntologyRelations2008-05-19T16:52:53Z<p>Alanr: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7056OntologyRelationsMay19MeetingNotes2008-05-19T16:23:05Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.<br />
<br />
Same or different identifiers for class/instance relations such as part_of?<br />
<br />
Numeric ids for RO terms?<br />
<br />
RO commits to BFO as upper level ontology<br />
<br />
RO will have separate identifiers for class level and instance level relations. (And different class level ids where the quantification is different). <br />
<br />
We will use numerical ids for RO terms.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7055OntologyRelationsMay19MeetingNotes2008-05-19T16:17:32Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.<br />
<br />
Same or different identifiers for class/instance relations such as part_of?<br />
<br />
Numeric ids for RO terms?<br />
<br />
RO commits to BFO as upper level ontology</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7054OntologyRelationsMay19MeetingNotes2008-05-19T15:49:54Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.<br />
<br />
Same or different identifiers for class/instance relations such as part_of?<br />
<br />
Numeric ids for RO terms?</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7053OntologyRelationsMay19MeetingNotes2008-05-19T15:38:32Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.<br />
<br />
The scope of RO is both type level relations and instance level relations. But we make clear which are which.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7052OntologyRelationsMay19MeetingNotes2008-05-19T15:27:19Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO<br />
<br />
On_the_surface_of lake, cell membrane - great if they were the same relation.</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7051OntologyRelationsMay19MeetingNotes2008-05-19T15:22:20Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?<br />
<br />
Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7050OntologyRelationsMay19MeetingNotes2008-05-19T15:11:55Z<p>Alanr: </p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelationsMay19MeetingNotes&diff=7049OntologyRelationsMay19MeetingNotes2008-05-19T15:10:46Z<p>Alanr: New page: What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. Sort out the case of cell membrane. Historical part of ...</p>
<hr />
<div>What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. <br />
<br />
Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7038OntologyRelations2008-05-17T23:09:06Z<p>Alanr: /* Guidelines and Goals */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* Overview and RCC8 (Melissa)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
**Example: tooth attachment use case (bona fide)<br />
* surrounded_by (Chris)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=Networks&diff=7036Networks2008-05-16T14:41:18Z<p>Alanr: /* Agenda */</p>
<hr />
<div>== Workshop on Ontologies of Cellular Networks ==<br />
<br />
This NCBO workshop is organized by Yves Lussier (Chicago/MAGNet), Alan Ruttenberg (Neurocommons) and Barry Smith (Buffalo/NCBO). It is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics].<br />
<br />
'''THIS EVENT IS NOW FULLY SUBSCRIBED.'''<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on ontologies of cellular networks.<br />
<br />
The goals of this workshop are:<br />
<br />
*1. to provide an introduction to the basic tools and methods of ontology <br />
*2. to foster networking of, and enhanced coordination between, those groups already working on ontologies of cellular networks<br />
*3. to identify problems which must be solved if ontology methods are to be extended to represent biological mechanisms in greater detail<br />
*4. to promote further ontology development in this area with the goal of accelerating our ability to understand basic biological phenomena and to leverage experimental data<br />
<br />
Potential topics for discussion include: <br />
<br />
*signalling pathways<br />
*metabolic pathways<br />
*regulatory networks<br />
*interaction networks<br />
*gene expression correlation networks<br />
*physiological networks<br />
*neurocurrent networks<br />
<br />
== Agenda ==<br />
<br />
'''Thursday, March 27, 2008''' <br />
<br />
* 9:00am Registration and Continental Breakfast<br />
<br />
* 9:30am Participant Self-Introductions<br />
<br />
* 10:00am '''Session 1 - Biology of Pathways and Networks (Moderator: Yves Lussier)'''<br />
<br />
::Chris Sander: Pathways and Networks: An Overview of the Science<br />
::Nancy Gough: [http://ontology.buffalo.edu/08/networks/Gough.ppt Challenges to Representing Pathways]<br />
<br />
* 11:00am Refreshment Break<br />
<br />
* 11:15am (Session 1, continued)<br />
<br />
::Richard Scheuermann: [http://ontology.buffalo.edu/08/networks/Scheuermann.ppt Biological Network Analysis and Representational Implications]<br />
::Yves Lussier: [http://ontology.buffalo.edu/08/networks/Lussier.pdf Resources for Multiscale Analysis of Cellular Networks and ECM]<br />
<br />
* 12:30pm Lunch Break<br />
<br />
* 1:30pm '''Session 2 - Introduction to Ontology (Moderator: Barry Smith)'''<br />
<br />
::Barry Smith: [http://ontology.buffalo.edu/08/networks/smith.ppt An Introduction to Biomedical Ontology]<br />
::Lindsay Cowell: [http://ontology.buffalo.edu/08/networks/cowell.ppt Using Ontologies to Represent Immunological Networks]<br />
::Jose L. V. Mejino, Jr.: [http://ontology.buffalo.edu/08/networks/mejino.ppt The Foundational Model of Anatomy (FMA) Ontology: Framework for Cellular and Subcellular Anatomy]<br />
<br />
* 3:30pm Refreshment Break<br />
* 3:45pm '''Session 3 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg) <br />
<br />
::Nigam Shah: [http://ontology.buffalo.edu/08/networks/Shah.ppt Computations using pathways and networks]<br />
::Andrea Splendini: [http://ontology.buffalo.edu/08/networks/Splendiani.pdf Using BioPAX Computationally]<br />
<br />
* 5:00pm End of Day 1 <br />
<br />
'''Friday, March 28, 2008'''<br />
<br />
* 8:30am Continental Breakfast<br />
<br />
* 9:00am Session 4: '''Current Approaches to Pathway and Network Ontologies (Moderator: Richard Scheuermann)'''<br />
<br />
::Markus Krummenacker: [http://ontology.buffalo.edu/08/networks/krummenacker.ppt The BioCyc Ontologies]<br />
::Ken Fukuda: [http://ontology.buffalo.edu/08/networks/fukuda.pdf The INOH Pathway Database: Curation, Annotation, Integration]<br />
::Erick Antezana: [http://ontology.buffalo.edu/08/networks/Antezana.ppt The Cell Cycle Ontology]<br />
<br />
* 10:30am Refreshment Break<br />
* 10:45am (Session 4, continued)<br />
<br />
::Peter D'Eustachio and Gopal Gopinathrao: [http://ontology.buffalo.edu/08/networks/Gopinathrao.ppt Representing Biological Processes: The Reactome Database]<br />
::Darren Natale: [http://ontology.buffalo.edu/08/networks/Natale.ppt Protein Ontology: Addressing the Need for Precision in Representing Protein Networks]<br />
<br />
* 12.30pm Lunch Break<br />
<br />
* 1:30pm '''Session 5 - Gaps in Pathway and Network Ontology (Moderator: Alan Ruttenberg)'''<br />
<br />
::Andrey Rzhetsky: [http://ontology.buffalo.edu/08/networks/Rzhetsky.ppt Text-Mining & Ontologies]<br />
::Oliver Ruebenacker: [http://ontology.buffalo.edu/08/networks/Ruebenacker.pdf Systems Biology Pathway Exchange]<br />
::Gopal Gopinathrao: [http://ontology.buffalo.edu/08/networks/Gopinathrao.ppt Gaps in Reactome]<br />
::Chris Sander: General Comments on Gaps between Pathways and Ontologies<br />
::Alan Ruttenberg: [http://www.bioontology.org/wiki/images/b/b7/Gaps.pdf Some Gaps of My Own: BioPAX-OBO Relationship, Identity, Definition of 'Pathway', Declarative Representations, Falsifiability, Entities]<br />
::Barry Smith: [http://ontology.buffalo.edu/08/networks/Smith2.ppt Pathways and Networks for Realists]<br />
::Open discussion.<br />
<br />
* 4:00pm End of Day 2<br />
<br />
==Confirmed Participants==<br />
<br />
Erick Antezana (VIB / Ghent University, Belgium)<br />
<br />
Mikel Egana Aranguren (University of Manchester, UK)<br />
<br />
Robert Arp (NCBO / University at Buffalo)<br />
<br />
Gary Bader (BioPAX / University of Toronto, Canada)<br />
<br />
Michael Blinov (Center of Cell Analysis & Modeling / University of Connecticut Health Center)<br />
<br />
Kei Cheung (Yale University / Center for Medical Informatics)<br />
<br />
Lindsay Cowell (Infectious Disease Ontology / Duke University Medical Center)<br />
<br />
Emek Demir (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Peter D'Eustachio (Reactome / New York University School of Medicine)<br />
<br />
Ken Fukuda (INOH Pathway Database / Computational Biology Research Center, Advanced Industrial Science & Technology, Japan)<br />
<br />
Louis Goldberg (Ontology Research Group / University at Buffalo)<br />
<br />
Gopal Gopinathrao (Stein Lab / Cold Spring Harbor Laboratory)<br />
<br />
Nancy Gough (Science Signaling, AAAS)<br />
<br />
Matt Holford (Yale University)<br />
<br />
Markus Krummenacker (SRI International)<br />
<br />
Yves Lussier (University of Chicago)<br />
<br />
Joanne S. Luciano (MITRE, BioPAX, BioPathways Consortium)<br />
<br />
Peter Lyster (NIGMS / National Institutes of Health)<br />
<br />
Avi Ma'ayan (Mount Sinai School of Medicine)<br />
<br />
Jose L. V. Mejino, Jr. (FMA Ontology / University of Washington, Seattle)<br />
<br />
Richard Morse (CHDI Management Inc. / CHDI Foundation Inc.)<br />
<br />
Josefina (Fina) Nash (Coriell Institute)<br />
<br />
Darren Natale (Protein Ontology / PIR, Georgetown University Medical Center)<br />
<br />
Elgar Pichler (BioPAX / AstraZeneca)<br />
<br />
Othel Rolle (Pfizer, Inc.) <br />
<br />
Oliver Ruebenacker (Center for Cell Analysis and Modeling / University of Connecticut Health Center)<br />
<br />
Alan Ruttenberg (BioPAX / Science Commons)<br />
<br />
Andrey Rzhetsky (University of Chicago)<br />
<br />
Chris Sander (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Richard Scheuermann (UT Southwestern Medical Center at Dallas)<br />
<br />
Nigam Shah (NCBO / Stanford University)<br />
<br />
Barry Smith (NCBO / University at Buffalo)<br />
<br />
Andrea Splendiani (BioPAX/Medical Informatics, University of Rennes, France)<br />
<br />
Balaji S. Srinivasan (Stanford University, Statistics)<br />
<br />
John Westbrook (Rutgers)<br />
<br />
Ulrike Wittig (EML Research gGmbH, Germany)<br />
<br />
Cathy Wu (Protein Ontology / PIR, Georgetown University Medical Center)<br />
<br />
==Venue / Lodging / Transportation==<br />
<br />
'''VENUE:'''<br />
The NCBO Workshop on Ontologies of Cellular Networks will take place on March 27-28, 2008 at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] (''Junior Ballroom''). <br />
<br />
<br />
'''LODGING:'''<br />
Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make room reservations either by calling 1-800-HILTONS and asking for the '''"National Center for Biomedical Ontology"''' block, or by entering group/convention code '''"NCB"''' when making reservations online at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] website. <br />
<br />
NOTE: To qualify for the special room block rate of $149 (+ tax) per night, reservations must be secured no later than '''Wednesday, March 5'''. After this date, reservations will be accepted based on availability and at prevailing rates.<br />
<br />
<br />
'''TRANSPORTATION / DRIVING DIRECTIONS TO VENUE:''' <br />
<br />
''FROM NEWARK AIRPORT:''<br />
<br />
HOTEL SHUTTLE: The Hilton Newark Airport Hotel provides complimentary shuttle service from (and to) the airport. When you arrive at the Newark Airport, follow signs to the Baggage Claim Area. Take the Airtrain to Airstation '''P4'''. The shuttle pickup is every 20 minutes from this location.<br />
<br />
TAXI: Typical minimum charge is USD 20.00<br />
<br />
DRIVING DIRECTIONS: Follow signs to airport exit, US Rte 1&9 N. to Haynes Ave. Take US Rte 1&9 S. After McClellan St. overpass, bear right to Service Road. The Hilton Hotel entrance is the 2nd driveway.<br />
<br />
<br />
''DRIVING DIRECTIONS FROM ELSEWHERE:''<br />
<br />
TRAVELLING SOUTHBOUND ON ROUTES 1 & 9: Local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right. <br />
<br />
TRAVELLING NORTHBOUND ON ROUTES 1 & 9: Exit at McClellan Street. At the base of the ramp, turn left, and the Hilton Hotel is on the right. <br />
<br />
FROM THE N.J. TURNPIKE NORTHBOUND: Take exit 13A. Get on Routes 1 & 9 North to the McClellan Street exit. At base of ramp, turn left and the Hilton Hotel is on the right. <br />
<br />
FROM THE N.J. TURNPIKE SOUTHBOUND: Take exit 14 to Routes 1 & 9 south, local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right.<br />
<br />
==Links ==<br />
<br />
* [http://groups.google.com/group/ontologies-of-cellular-networks?hl=en Google Groups discussion]<br />
<br />
* [http://sig.biostr.washington.edu/projects/fm/ FMA: Foundational Model of Anatomy]<br />
<br />
* [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]<br />
<br />
* [http://obofoundry.org OBO Foundry]<br />
<br />
==Literature==<br />
<br />
*[http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]<br />
<br />
*[http://xml.coverpages.org/OntologyExchange.html An evaluation of ontology exchange languages for bioinformatics]<br />
<br />
*[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Coordinated Evolution of Ontologies to Support Biomedical Data Integration]<br />
<br />
*Green ML and Karp PD: [http://www.ncbi.nlm.nih.gov/pubmed/16893953?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The outcomes of pathway database computations depend on pathway ontology]<br />
<br />
==Addendum: Do Mountains Exist?==<br />
<br />
This paper:<br />
<br />
::Barry Smith and David M. Mark, [http://ontology.buffalo.edu/smith/articles/Mountains.pdf “Do Mountains Exist? Towards an Ontology of Landforms”], Environment and Planning B (Planning and Design), 30(3) (2003), 411–427.<br />
<br />
defends the thesis that mountains do indeed exist. But it argues that this assertion is non-trivial, in virtue of the fact that mountains have no determinate boundaries. <br />
<br />
Similarly in the case of pathways and networks; pathways and networks do indeed exist -- but different groups of researchers place their boundaries in different places. To find ways to pool their data these different groups would need to acknowledge the differences in demarcation on which their pathway and network representations rest. See presentation [http://ontology.buffalo.edu/08/networks/smith2.ppt Pathways and Networks for Realists].</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=File:Gaps.pdf&diff=7035File:Gaps.pdf2008-05-16T14:39:38Z<p>Alanr: </p>
<hr />
<div></div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=Networks&diff=6673Networks2008-03-25T11:26:01Z<p>Alanr: </p>
<hr />
<div>== Workshop on Ontologies of Cellular Networks ==<br />
<br />
This NCBO workshop is organized by Yves Lussier (Chicago/MAGNet), Alan Ruttenberg (Neurocommons) and Barry Smith (Buffalo/NCBO). It is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics].<br />
<br />
'''THIS EVENT IS NOW FULLY SUBSCRIBED.'''<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on ontologies of cellular networks.<br />
<br />
The goals of this workshop are:<br />
<br />
*1. to provide an introduction to the basic tools and methods of ontology <br />
*2. to foster networking of, and enhanced coordination between, those groups already working on ontologies of cellular networks<br />
*3. to identify problems which must be solved if ontology methods are to be extended to represent biological mechanisms in greater detail<br />
*4. to promote further ontology development in this area with the goal of accelerating our ability to understand basic biological phenomena and to leverage experimental data<br />
<br />
Potential topics for discussion include: <br />
<br />
*signalling pathways<br />
*metabolic pathways<br />
*regulatory networks<br />
*interaction networks<br />
*gene expression correlation networks<br />
*physiological networks<br />
*neurocurrent networks<br />
<br />
== Agenda ==<br />
<br />
'''Thursday, March 27, 2008''' <br />
<br />
* 9:00am Registration and Continental Breakfast<br />
<br />
* 9:30am Participant Self-Introductions<br />
<br />
* 10:00am '''Session 1 - Biology of Pathways and Networks (Moderator: Yves Lussier)'''<br />
<br />
::Chris Sander: Pathways and Networks: An Overview of the Science<br />
::Balaji S. Srinivasan: Current Progress in Network Research<br />
<br />
* 11:00am Refreshment Break<br />
<br />
* 11:15am (Session 1, continued)<br />
<br />
::Richard Scheuermann: Networks and Modularity<br />
::Yves Lussier: The Extracellular Matrix<br />
<br />
* 12:30pm Lunch Break<br />
<br />
* 1:30pm '''Session 2 - Introduction to Ontology (Moderator: Barry Smith)'''<br />
<br />
::Lindsay Cowell: Immune System Ontology<br />
::Jose L. V. Mejino, Jr.: The FMA: A Framework for Subcellular Network Anatomy<br />
::Barry Smith: Pathways and Networks for Realists<br />
<br />
* 3:30pm Refreshment Break<br />
* 3:45pm '''Session 3 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg) <br />
<br />
::Nigam Shah: Requirements for Representing Biological Processes as Pathways and Networks<br />
::Andrea Splendini: Using BioPAX Computationally<br />
<br />
* 5:00pm End of Day 1 <br />
<br />
'''Friday, March 28, 2008'''<br />
<br />
* 8:30am Continental Breakfast<br />
<br />
* 9:00am Session 4: '''Current Approaches to Pathway and Network Ontologies (Moderator: Richard Scheuermann)'''<br />
<br />
::Markus Krummenacker: The BioCyc Ontologies<br />
::Ken Fukuda: The INOH Pathway Database<br />
<br />
* 10:30am Refreshment Break<br />
* 10:45am (Session 4, continued)<br />
<br />
::Peter D'Eustachio: Reactome<br />
::Gopal Gopinathrao: Gaps in Reactome<br />
::Darren Natale: Protein Ontology: Addressing the Need for Precision in Representing Protein Networks<br />
<br />
* 12.30pm Lunch Break<br />
<br />
* 1:30pm '''Session 5 - Gaps in Pathway and Network Ontology (Moderator: Alan Ruttenberg)'''<br />
<br />
::Open discussion; presenters and topics to be determined <br />
<br />
* 4:00pm End of Day 2<br />
<br />
==Confirmed Participants==<br />
<br />
Erick Antezana (VIB / Ghent University, Belgium)<br />
<br />
Mikel Egana Aranguren (University of Manchester, UK)<br />
<br />
Robert Arp (NCBO / University at Buffalo)<br />
<br />
Gary Bader (BioPAX / University of Toronto, Canada)<br />
<br />
Michael Blinov (Center of Cell Analysis & Modeling / University of Connecticut Health Center)<br />
<br />
Kei Cheung (Yale University / Center for Medical Informatics)<br />
<br />
Lindsay Cowell (Infectious Disease Ontology / Duke University Medical Center)<br />
<br />
Emek Demir (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Peter D'Eustachio (Reactome / New York University School of Medicine)<br />
<br />
Ken Fukuda (INOH Pathway Database / Computational Biology Research Center, Advanced Industrial Science & Technology, Japan)<br />
<br />
Louis Goldberg (Ontology Research Group / University at Buffalo)<br />
<br />
Gopal Gopinathrao (Stein Lab / Cold Spring Harbor Laboratory)<br />
<br />
Nancy Gough (Science Signaling, AAAS)<br />
<br />
Matt Holford (Yale University)<br />
<br />
Markus Krummenacker (SRI International)<br />
<br />
Yves Lussier (University of Chicago)<br />
<br />
Peter Lyster (NIGMS / National Institutes of Health)<br />
<br />
Avi Ma'ayan (Mount Sinai School of Medicine)<br />
<br />
Jose L. V. Mejino, Jr. (FMA Ontology / University of Washington, Seattle)<br />
<br />
Richard Morse (CHDI Management Inc. / CHDI Foundation Inc.)<br />
<br />
Josefina (Fina) Nash (Coriell Institute)<br />
<br />
Darren Natale (Protein Ontology / PIR, Georgetown University Medical Center)<br />
<br />
Elgar Pichler (BioPAX / AstraZeneca)<br />
<br />
Othel Rolle (Pfizer, Inc.) <br />
<br />
Oliver Ruebenacker (Center for Cell Analysis and Modeling / University of Connecticut Health Center)<br />
<br />
Alan Ruttenberg (BioPAX / Science Commons)<br />
<br />
Andrey Rzhetsky (University of Chicago)<br />
<br />
Chris Sander (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Richard Scheuermann (UT Southwestern Medical Center at Dallas)<br />
<br />
Nigam Shah (NCBO / Stanford University)<br />
<br />
Barry Smith (NCBO / University at Buffalo)<br />
<br />
Andrea Splendiani (BioPAX/Medical Informatics, University of Rennes, France)<br />
<br />
Balaji S. Srinivasan (Stanford University, Statistics)<br />
<br />
John Westbrook (Rutgers)<br />
<br />
Ulrike Wittig (EML Research gGmbH, Germany)<br />
<br />
Cathy Wu (Protein Ontology / PIR, Georgetown University Medical Center)<br />
<br />
==Venue / Lodging / Transportation==<br />
<br />
'''VENUE:'''<br />
The NCBO Workshop on Ontologies of Cellular Networks will take place on March 27-28, 2008 at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] (''Junior Ballroom''). <br />
<br />
<br />
'''LODGING:'''<br />
Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make room reservations either by calling 1-800-HILTONS and asking for the '''"National Center for Biomedical Ontology"''' block, or by entering group/convention code '''"NCB"''' when making reservations online at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] website. <br />
<br />
NOTE: To qualify for the special room block rate of $149 (+ tax) per night, reservations must be secured no later than '''Wednesday, March 5'''. After this date, reservations will be accepted based on availability and at prevailing rates.<br />
<br />
<br />
'''TRANSPORTATION / DRIVING DIRECTIONS TO VENUE:''' <br />
<br />
''FROM NEWARK AIRPORT:''<br />
<br />
HOTEL SHUTTLE: The Hilton Newark Airport Hotel provides complimentary shuttle service from (and to) the airport. When you arrive at the Newark Airport, follow signs to the Baggage Claim Area. Take the Airtrain to Airstation '''P4'''. The shuttle pickup is every 20 minutes from this location.<br />
<br />
TAXI: Typical minimum charge is USD 20.00<br />
<br />
DRIVING DIRECTIONS: Follow signs to airport exit, US Rte 1&9 N. to Haynes Ave. Take US Rte 1&9 S. After McClellan St. overpass, bear right to Service Road. The Hilton Hotel entrance is the 2nd driveway.<br />
<br />
<br />
''DRIVING DIRECTIONS FROM ELSEWHERE:''<br />
<br />
TRAVELLING SOUTHBOUND ON ROUTES 1 & 9: Local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right. <br />
<br />
TRAVELLING NORTHBOUND ON ROUTES 1 & 9: Exit at McClellan Street. At the base of the ramp, turn left, and the Hilton Hotel is on the right. <br />
<br />
FROM THE N.J. TURNPIKE NORTHBOUND: Take exit 13A. Get on Routes 1 & 9 North to the McClellan Street exit. At base of ramp, turn left and the Hilton Hotel is on the right. <br />
<br />
FROM THE N.J. TURNPIKE SOUTHBOUND: Take exit 14 to Routes 1 & 9 south, local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right.<br />
<br />
==Links ==<br />
<br />
* [http://sig.biostr.washington.edu/projects/fm/ FMA: Foundational Model of Anatomy]<br />
<br />
* [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]<br />
<br />
* [http://obofoundry.org OBO Foundry]<br />
<br />
==Literature==<br />
<br />
[http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]<br />
<br />
[http://xml.coverpages.org/OntologyExchange.html An evaluation of ontology exchange languages for bioinformatics]<br />
<br />
[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Coordinated Evolution of Ontologies to Support Biomedical Data Integration]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=Networks&diff=6672Networks2008-03-23T23:30:09Z<p>Alanr: </p>
<hr />
<div>== Workshop on Ontologies of Cellular Networks ==<br />
<br />
This NCBO workshop is organized by Yves Lussier (Chicago/MAGNet), Alan Ruttenberg (Neurocommons) and Barry Smith (Buffalo/NCBO). It is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics].<br />
<br />
'''THIS EVENT IS NOW FULLY SUBSCRIBED.'''<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on ontologies of cellular networks.<br />
<br />
The goals of this workshop are:<br />
<br />
*1. to provide an introduction to the basic tools and methods of ontology <br />
*2. to foster networking of, and enhanced coordination between, those groups already working on ontologies of cellular networks<br />
*3. to identify problems which must be solved if ontology methods are to be extended to represent biological mechanisms in greater detail<br />
*4. to promote further ontology development in this area with the goal of accelerating our ability to understand basic biological phenomena and to leverage experimental data<br />
<br />
Potential topics for discussion include: <br />
<br />
*signalling pathways<br />
*metabolic pathways<br />
*regulatory networks<br />
*interaction networks<br />
*gene expression correlation networks<br />
*physiological networks<br />
*neurocurrent networks<br />
<br />
== Agenda ==<br />
<br />
'''Thursday, March 27, 2008''' <br />
<br />
* 9:00am Registration and Continental Breakfast<br />
<br />
* 9:30am Participant Self-Introductions<br />
<br />
* 10:00am '''Session 1 - Biology of Pathways and Networks (Moderator: Yves Lussier)'''<br />
<br />
::Chris Sander: Pathways and Networks: An Overview of the Science<br />
::Balaji S. Srinivasan: Current Progress in Network Research<br />
<br />
* 11:00am Refreshment Break<br />
<br />
* 11:15am (Session 1, continued)<br />
<br />
::Richard Scheuermann: Networks and Modularity<br />
::Yves Lussier: The Extracellular Matrix<br />
<br />
* 12:30pm Lunch Break<br />
<br />
* 1:30pm '''Session 2 - Introduction to Ontology (Moderator: Barry Smith)'''<br />
<br />
::Lindsay Cowell: Immune System Ontology<br />
::Jose L. V. Mejino, Jr.: The FMA: A Framework for Subcellular Network Anatomy<br />
::Barry Smith: Pathways and Networks for Realists<br />
<br />
* 3:30pm Refreshment Break<br />
* 3:45pm '''Session 3 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg) <br />
<br />
::Nigam Shah: Requirements for Representing Biological Processes as Pathways and Networks<br />
::Andrea Splendini: Using BioPAX Computationally<br />
<br />
* 5:00pm End of Day 1 <br />
<br />
'''Friday, March 28, 2008'''<br />
<br />
* 8:30am Continental Breakfast<br />
<br />
* 9:00am Session 4: '''Current Approaches to Pathway and Network Ontologies (Moderator: Richard Scheuermann)'''<br />
<br />
::Markus Krummenacker: The BioCyc Ontologies<br />
::Ken Fukuda: The INOH Pathway Database<br />
<br />
* 10:30am Refreshment Break<br />
* 10:45am (Session 4, continued)<br />
<br />
::Peter D'Eustachio: Reactome<br />
::Darren Natale: Protein Ontology: Addressing the Need for Precision in Representing Protein Networks<br />
<br />
* 12.30pm Lunch Break<br />
<br />
* 1:30pm '''Session 5 - Gaps in Pathway and Network Ontology (Moderator: Alan Ruttenberg)'''<br />
<br />
::Gopal Gopinathrao: Gaps in Reactome<br />
::Andrey Rzhetsky: Ontological Problems in Text Mining<br />
<br />
::Open discussion; Topics to be determined <br />
<br />
* 4:00pm End of Day 2<br />
<br />
==Confirmed Participants==<br />
<br />
Erick Antezana (VIB / Ghent University, Belgium)<br />
<br />
Mikel Egana Aranguren (University of Manchester, UK)<br />
<br />
Robert Arp (NCBO / University at Buffalo)<br />
<br />
Gary Bader (BioPAX / University of Toronto, Canada)<br />
<br />
Michael Blinov (Center of Cell Analysis & Modeling / University of Connecticut Health Center)<br />
<br />
Kei Cheung (Yale University / Center for Medical Informatics)<br />
<br />
Lindsay Cowell (Infectious Disease Ontology / Duke University Medical Center)<br />
<br />
Emek Demir (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Peter D'Eustachio (Reactome / New York University School of Medicine)<br />
<br />
Ken Fukuda (INOH Pathway Database / Computational Biology Research Center, Advanced Industrial Science & Technology, Japan)<br />
<br />
Louis Goldberg (Ontology Research Group / University at Buffalo)<br />
<br />
Gopal Gopinathrao (Stein Lab / Cold Spring Harbor Laboratory)<br />
<br />
Nancy Gough (Science Signaling, AAAS)<br />
<br />
Matt Holford (Yale University)<br />
<br />
Markus Krummenacker (SRI International)<br />
<br />
Yves Lussier (University of Chicago)<br />
<br />
Peter Lyster (NIGMS / National Institutes of Health)<br />
<br />
Avi Ma'ayan (Mount Sinai School of Medicine)<br />
<br />
Jose L. V. Mejino, Jr. (FMA Ontology / University of Washington, Seattle)<br />
<br />
Richard Morse (CHDI Management Inc. / CHDI Foundation Inc.)<br />
<br />
Josefina (Fina) Nash (Coriell Institute)<br />
<br />
Darren Natale (Protein Ontology / PIR, Georgetown University Medical Center)<br />
<br />
Elgar Pichler (BioPAX / AstraZeneca)<br />
<br />
Othel Rolle (Pfizer, Inc.) <br />
<br />
Oliver Ruebenacker (Center for Cell Analysis and Modeling / University of Connecticut Health Center)<br />
<br />
Alan Ruttenberg (BioPAX / Science Commons)<br />
<br />
Andrey Rzhetsky (University of Chicago)<br />
<br />
Chris Sander (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Richard Scheuermann (UT Southwestern Medical Center at Dallas)<br />
<br />
Nigam Shah (NCBO / Stanford University)<br />
<br />
Barry Smith (NCBO / University at Buffalo)<br />
<br />
Andrea Splendiani (BioPAX/Medical Informatics, University of Rennes, France)<br />
<br />
Balaji S. Srinivasan (Stanford University, Statistics)<br />
<br />
John Westbrook (Rutgers)<br />
<br />
Ulrike Wittig (EML Research gGmbH, Germany)<br />
<br />
Cathy Wu (Protein Ontology / PIR, Georgetown University Medical Center)<br />
<br />
==Venue / Lodging / Transportation==<br />
<br />
'''VENUE:'''<br />
The NCBO Workshop on Ontologies of Cellular Networks will take place on March 27-28, 2008 at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] (''Junior Ballroom''). <br />
<br />
<br />
'''LODGING:'''<br />
Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make room reservations either by calling 1-800-HILTONS and asking for the '''"National Center for Biomedical Ontology"''' block, or by entering group/convention code '''"NCB"''' when making reservations online at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] website. <br />
<br />
NOTE: To qualify for the special room block rate of $149 (+ tax) per night, reservations must be secured no later than '''Wednesday, March 5'''. After this date, reservations will be accepted based on availability and at prevailing rates.<br />
<br />
<br />
'''TRANSPORTATION / DRIVING DIRECTIONS TO VENUE:''' <br />
<br />
''FROM NEWARK AIRPORT:''<br />
<br />
HOTEL SHUTTLE: The Hilton Newark Airport Hotel provides complimentary shuttle service from (and to) the airport. When you arrive at the Newark Airport, follow signs to the Baggage Claim Area. Take the Airtrain to Airstation '''P4'''. The shuttle pickup is every 20 minutes from this location.<br />
<br />
TAXI: Typical minimum charge is USD 20.00<br />
<br />
DRIVING DIRECTIONS: Follow signs to airport exit, US Rte 1&9 N. to Haynes Ave. Take US Rte 1&9 S. After McClellan St. overpass, bear right to Service Road. The Hilton Hotel entrance is the 2nd driveway.<br />
<br />
<br />
''DRIVING DIRECTIONS FROM ELSEWHERE:''<br />
<br />
TRAVELLING SOUTHBOUND ON ROUTES 1 & 9: Local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right. <br />
<br />
TRAVELLING NORTHBOUND ON ROUTES 1 & 9: Exit at McClellan Street. At the base of the ramp, turn left, and the Hilton Hotel is on the right. <br />
<br />
FROM THE N.J. TURNPIKE NORTHBOUND: Take exit 13A. Get on Routes 1 & 9 North to the McClellan Street exit. At base of ramp, turn left and the Hilton Hotel is on the right. <br />
<br />
FROM THE N.J. TURNPIKE SOUTHBOUND: Take exit 14 to Routes 1 & 9 south, local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right.<br />
<br />
==Links ==<br />
<br />
* [http://sig.biostr.washington.edu/projects/fm/ FMA: Foundational Model of Anatomy]<br />
<br />
* [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]<br />
<br />
* [http://obofoundry.org OBO Foundry]<br />
<br />
==Literature==<br />
<br />
[http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]<br />
<br />
[http://xml.coverpages.org/OntologyExchange.html An evaluation of ontology exchange languages for bioinformatics]<br />
<br />
[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Coordinated Evolution of Ontologies to Support Biomedical Data Integration]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=Networks&diff=6671Networks2008-03-23T23:29:30Z<p>Alanr: </p>
<hr />
<div>== Workshop on Ontologies of Cellular Networks ==<br />
<br />
This NCBO workshop is organized by Yves Lussier (Chicago/MAGNet), Alan Ruttenberg (Neurocommons) and Barry Smith (Buffalo/NCBO). It is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics].<br />
<br />
'''THIS EVENT IS NOW FULLY SUBSCRIBED.'''<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on ontologies of cellular networks.<br />
<br />
The goals of this workshop are:<br />
<br />
*1. to provide an introduction to the basic tools and methods of ontology <br />
*2. to foster networking of, and enhanced coordination between, those groups already working on ontologies of cellular networks<br />
*3. to identify problems which must be solved if ontology methods are to be extended to represent biological mechanisms in greater detail<br />
*4. to promote further ontology development in this area with the goal of accelerating our ability to understand basic biological phenomena and to leverage experimental data<br />
<br />
Potential topics for discussion include: <br />
<br />
*signalling pathways<br />
*metabolic pathways<br />
*regulatory networks<br />
*interaction networks<br />
*gene expression correlation networks<br />
*physiological networks<br />
*neurocurrent networks<br />
<br />
== Agenda ==<br />
<br />
'''Thursday, March 27, 2008''' <br />
<br />
* 9:00am Registration and Continental Breakfast<br />
<br />
* 9:30am Participant Self-Introductions<br />
<br />
* 10:00am '''Session 1 - Biology of Pathways and Networks (Moderator: Yves Lussier)'''<br />
<br />
::Chris Sander: Pathways and Networks: An Overview of the Science<br />
::Balaji S. Srinivasan: Current Progress in Network Research<br />
<br />
* 11:00am Refreshment Break<br />
<br />
* 11:15am (Session 1, continued)<br />
<br />
::Richard Scheuermann: Networks and Modularity<br />
::Yves Lussier: The Extracellular Matrix<br />
<br />
* 12:30pm Lunch Break<br />
<br />
* 1:30pm '''Session 2 - Introduction to Ontology (Moderator: Barry Smith)'''<br />
<br />
::Lindsay Cowell: Immune System Ontology<br />
::Jose L. V. Mejino, Jr.: The FMA: A Framework for Subcellular Network Anatomy<br />
::Barry Smith: Pathways and Networks for Realists<br />
<br />
* 3:30pm Refreshment Break<br />
* 3:45pm '''Session 3 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg) <br />
<br />
::Nigam Shah: Requirements for Representing Biological Processes as Pathways and Networks<br />
::Andrea Splendini: Using BioPAX Computationally<br />
<br />
* 5:00pm End of Day 1 <br />
<br />
'''Friday, March 28, 2008'''<br />
<br />
* 8:30am Continental Breakfast<br />
<br />
* 9:00am Session 4: '''Current Approaches to Pathway and Network Ontologies (Moderator: Richard Scheuermann)'''<br />
<br />
::Markus Krummenacker: The BioCyc Ontologies<br />
::Ken Fukuda: The INOH Pathway Database<br />
<br />
* 10:30am Refreshment Break<br />
* 10:45am (Session 4, continued)<br />
<br />
::Peter D'Eustachio: Reactome<br />
::Darren Natale: Protein Ontology: Addressing the Need for Precision in Representing Protein Networks<br />
<br />
* 12.30pm Lunch Break<br />
<br />
* 1:30pm '''Session 5 - Gaps in Pathway and Network Ontology (Moderator: Alan Ruttenberg)'''<br />
<br />
::Gopal Gopinathrao: Gaps in Reactome<br />
::Andrey Rzhetsky: Ontological Problems in Text Mining<br />
<br />
::Open discussion; presenters and <br />
<br />
* 4:00pm End of Day 2<br />
<br />
==Confirmed Participants==<br />
<br />
Erick Antezana (VIB / Ghent University, Belgium)<br />
<br />
Mikel Egana Aranguren (University of Manchester, UK)<br />
<br />
Robert Arp (NCBO / University at Buffalo)<br />
<br />
Gary Bader (BioPAX / University of Toronto, Canada)<br />
<br />
Michael Blinov (Center of Cell Analysis & Modeling / University of Connecticut Health Center)<br />
<br />
Kei Cheung (Yale University / Center for Medical Informatics)<br />
<br />
Lindsay Cowell (Infectious Disease Ontology / Duke University Medical Center)<br />
<br />
Emek Demir (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Peter D'Eustachio (Reactome / New York University School of Medicine)<br />
<br />
Ken Fukuda (INOH Pathway Database / Computational Biology Research Center, Advanced Industrial Science & Technology, Japan)<br />
<br />
Louis Goldberg (Ontology Research Group / University at Buffalo)<br />
<br />
Gopal Gopinathrao (Stein Lab / Cold Spring Harbor Laboratory)<br />
<br />
Nancy Gough (Science Signaling, AAAS)<br />
<br />
Matt Holford (Yale University)<br />
<br />
Markus Krummenacker (SRI International)<br />
<br />
Yves Lussier (University of Chicago)<br />
<br />
Peter Lyster (NIGMS / National Institutes of Health)<br />
<br />
Avi Ma'ayan (Mount Sinai School of Medicine)<br />
<br />
Jose L. V. Mejino, Jr. (FMA Ontology / University of Washington, Seattle)<br />
<br />
Richard Morse (CHDI Management Inc. / CHDI Foundation Inc.)<br />
<br />
Josefina (Fina) Nash (Coriell Institute)<br />
<br />
Darren Natale (Protein Ontology / PIR, Georgetown University Medical Center)<br />
<br />
Elgar Pichler (BioPAX / AstraZeneca)<br />
<br />
Othel Rolle (Pfizer, Inc.) <br />
<br />
Oliver Ruebenacker (Center for Cell Analysis and Modeling / University of Connecticut Health Center)<br />
<br />
Alan Ruttenberg (BioPAX / Science Commons)<br />
<br />
Andrey Rzhetsky (University of Chicago)<br />
<br />
Chris Sander (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Richard Scheuermann (UT Southwestern Medical Center at Dallas)<br />
<br />
Nigam Shah (NCBO / Stanford University)<br />
<br />
Barry Smith (NCBO / University at Buffalo)<br />
<br />
Andrea Splendiani (BioPAX/Medical Informatics, University of Rennes, France)<br />
<br />
Balaji S. Srinivasan (Stanford University, Statistics)<br />
<br />
John Westbrook (Rutgers)<br />
<br />
Ulrike Wittig (EML Research gGmbH, Germany)<br />
<br />
Cathy Wu (Protein Ontology / PIR, Georgetown University Medical Center)<br />
<br />
==Venue / Lodging / Transportation==<br />
<br />
'''VENUE:'''<br />
The NCBO Workshop on Ontologies of Cellular Networks will take place on March 27-28, 2008 at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] (''Junior Ballroom''). <br />
<br />
<br />
'''LODGING:'''<br />
Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make room reservations either by calling 1-800-HILTONS and asking for the '''"National Center for Biomedical Ontology"''' block, or by entering group/convention code '''"NCB"''' when making reservations online at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] website. <br />
<br />
NOTE: To qualify for the special room block rate of $149 (+ tax) per night, reservations must be secured no later than '''Wednesday, March 5'''. After this date, reservations will be accepted based on availability and at prevailing rates.<br />
<br />
<br />
'''TRANSPORTATION / DRIVING DIRECTIONS TO VENUE:''' <br />
<br />
''FROM NEWARK AIRPORT:''<br />
<br />
HOTEL SHUTTLE: The Hilton Newark Airport Hotel provides complimentary shuttle service from (and to) the airport. When you arrive at the Newark Airport, follow signs to the Baggage Claim Area. Take the Airtrain to Airstation '''P4'''. The shuttle pickup is every 20 minutes from this location.<br />
<br />
TAXI: Typical minimum charge is USD 20.00<br />
<br />
DRIVING DIRECTIONS: Follow signs to airport exit, US Rte 1&9 N. to Haynes Ave. Take US Rte 1&9 S. After McClellan St. overpass, bear right to Service Road. The Hilton Hotel entrance is the 2nd driveway.<br />
<br />
<br />
''DRIVING DIRECTIONS FROM ELSEWHERE:''<br />
<br />
TRAVELLING SOUTHBOUND ON ROUTES 1 & 9: Local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right. <br />
<br />
TRAVELLING NORTHBOUND ON ROUTES 1 & 9: Exit at McClellan Street. At the base of the ramp, turn left, and the Hilton Hotel is on the right. <br />
<br />
FROM THE N.J. TURNPIKE NORTHBOUND: Take exit 13A. Get on Routes 1 & 9 North to the McClellan Street exit. At base of ramp, turn left and the Hilton Hotel is on the right. <br />
<br />
FROM THE N.J. TURNPIKE SOUTHBOUND: Take exit 14 to Routes 1 & 9 south, local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right.<br />
<br />
==Links ==<br />
<br />
* [http://sig.biostr.washington.edu/projects/fm/ FMA: Foundational Model of Anatomy]<br />
<br />
* [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]<br />
<br />
* [http://obofoundry.org OBO Foundry]<br />
<br />
==Literature==<br />
<br />
[http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]<br />
<br />
[http://xml.coverpages.org/OntologyExchange.html An evaluation of ontology exchange languages for bioinformatics]<br />
<br />
[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Coordinated Evolution of Ontologies to Support Biomedical Data Integration]</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=DRAFT_AGENDA&diff=6484DRAFT AGENDA2008-02-04T19:08:41Z<p>Alanr: </p>
<hr />
<div>== Preliminary Agenda ==<br />
<br />
'''Thursday, March 27, 2008''' <br />
<br />
* 9:00am Registration and Continental Breakfast<br />
<br />
* 9:30am Participant Self-Introductions<br />
<br />
* 10:00am '''Session 1 - Biology of Pathways and Networks (Moderator: Yves Lussier)'''<br />
<br />
:Potential presenters: <br />
::Fiona Brinkman<br />
::Nancy Gough<br />
::Yves Lussier<br />
::Chris Sander <br />
::Stuart Sealfon<br />
<br />
:Potential topics: <br />
::signalling pathways, metabolic pathways, ...<br />
::regulatory networks, interaction networks, gene expression correlation networks, physiological networks, neurocurrent networks, water balance networks, social networks, co-citation networks ...)<br />
::types of regulation (hormone regulation, organismal regulation, thermal regulation, blood pressure regulation ...)<br />
::granularity (molecular, cellular, physiological) ...<br />
::cellular networks and their surroundings: tissues, the extracellular matrix, and cell-environment interactions<br />
* 11:00am Refreshment Break<br />
* 11:15am <br />
<br />
* 12:30pm Lunch Break<br />
<br />
* 1:30pm '''Session 2 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg) <br />
<br />
:Potential presenters: <br />
::Peter Lyster<br />
::Avi Ma'ayan<br />
::Andre Rhzetsky<br />
::Oliver Ruebenacker<br />
::Richard Scheuermann<br />
::Andrea Splendiani <br />
<br />
* 3:30pm Refreshment Break<br />
* 3:45pm '''Session 3 - Introduction to Ontology (Moderator: Barry Smith)'''<br />
<br />
:Potential presenters<br />
::Lindsay Cowell<br />
::Barry Smith<br />
::J. L. E. Mejino Jr.<br />
<br />
* 5:00pm End of Day 1 <br />
<br />
'''Friday, March 28, 2008 - NETWORK DAY'''<br />
<br />
* 8:30am Continental Breakfast<br />
<br />
* 9:00am Session 4: '''Current Approaches to Pathway and Network Ontology (Moderator: Richard Scheuermann)'''<br />
<br />
:Potential presenters:<br />
::Bill Bug<br />
::Peter d'Eustachio: Reactome<br />
::Ken Fukuda: INOH Pathway Database<br />
::Darren Natale: Protein Ontology<br />
::Balaji S. Srinivasan<br />
<br />
* 10:45am Refreshment Break<br />
* 11:00am <br />
* 12.30pm Lunch Break<br />
<br />
* 1:30 '''Session 5 - Gaps in Network Ontology (Moderator: Alan Ruttenberg)'''<br />
<br />
:Open discussion; presenters and topics to be decided <br />
::(example:) Approaches to extending the OBO Foundry to include pathway and network ontologies <br />
<br />
* 4:00pm End of Day 2</div>Alanrhttps://www.bioontology.org//mediawiki/index.php?title=Networks&diff=6472Networks2008-02-04T04:38:04Z<p>Alanr: </p>
<hr />
<div>== Workshop on Ontologies of Cellular Networks ==<br />
To ensure highly interactive and productive sessions, the number of workshop participants will be limited. If you are interested in participating, please contact: [mailto:phismith@buffalo.edu Barry Smith]<br />
<br />
This workshop is organized by Yves Lussier (Chicago/MAGNet), Alan Ruttenberg (Neurocommons) and Barry Smith (Buffalo/NCBO). It is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics].<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on ontologies of cellular networks.<br />
<br />
The goals of this workshop are:<br />
<br />
*1. to provide an introduction to the basic tools and methods of ontology <br />
*2. to foster networking of, and enhanced coordination between, those groups already working on ontologies of cellular networks<br />
*3. to identify problems which must be solved if ontology methods are to be extended to represent biological mechanisms in greater detail<br />
*4. to promote further ontology development in this area with the goal of accelerating our ability to understand basic biological phenomena and to leverage experimental data<br />
<br />
== Preliminary Agenda ==<br />
<br />
'''Thursday, March 27, 2008''' <br />
<br />
* 9:00am Registration and Continental Breakfast<br />
<br />
* 10:00am Session 1 - Introductions<br />
''Moderator:''<br />
* 10:00am Participant Self-Introductions<br />
* 10:15am Introduction to Ontology<br />
* 10:45am The OBO Foundry<br />
* 11:15am Refreshment Break<br />
* 11:45am <br />
<br />
* 12:45pm Lunch Break<br />
<br />
* 2:00pm Session 2 - Cellular Networks and Cellular Network Data<br />
''Moderator:''<br />
<br />
* 3:15pm Refreshment Break<br />
<br />
* 5:00pm End of Day 1 <br />
<br />
<br />
'''Friday, March 28, 2008''' <br />
<br />
* 8:30am Continental Breakfast<br />
<br />
* 9:00am Session 3 - Ontologies of Cellular Networks: Alternative Approaches <br />
''Moderator:''<br />
<br />
* 10:45am Refreshment Break<br />
<br />
* Session 4 - <br />
''Moderator:'' <br />
<br />
* 12:45pm Lunch Break<br />
<br />
* 2:00 Session 5 - Ontologies of Cellular Networks: The Next Steps<br />
''Moderator: ''<br />
<br />
* 4:00pm End of Day 2<br />
<br />
==Participants==<br />
<br />
''Participants will include:''<br />
<br />
Robert Arp (NCBO / University at Buffalo)<br />
<br />
Gary Bader (BioPAX / University of Toronto)<br />
<br />
Helen Berman (Protein Data Bank / Rutgers University)<br />
<br />
William Bug (BIRN Ontology Task Force, UC San Diego)<br />
<br />
Kei Cheung (Yale Center for Medical Informatics)<br />
<br />
Lindsay Cowell (Infectious Disease Ontology / Duke University)<br />
<br />
Emek Demir (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Peter D'Eustachio (Reactome / New York University)<br />
<br />
Ken Ichiro Fukuda (INOH Pathway Database, Tokyo)<br />
<br />
Louis Goldberg (Ontology Research Group / University at Buffalo)<br />
<br />
Gopal Gopinathrao (Reactome / Cold Spring Harbor Laboratories)<br />
<br />
Nancy Gough (''Science'')<br />
<br />
Joanne Luciano (BioPAX / Harvard Medical School)<br />
<br />
Peter Lyster (NIGMS / National Institutes of Health)<br />
<br />
Avi Ma'ayan (Mount Sinai School of Medicine)<br />
<br />
J. L. E. Mejino, Jr. (FMA Ontology / University of Washington, Seattle)<br />
<br />
Darren Natale (Protein Ontology / PIR, Georgetown University)<br />
<br />
Oliver Ruebenacker (Center for Cell Analysis and Modelling / University of Connecticut Health Center)<br />
<br />
Alan Ruttenberg (BioPAX / Science Commons)<br />
<br />
Andrey Rzhetsky (University of Chicago)<br />
<br />
Chris Sander (BioPAX / Memorial Sloan-Kettering Cancer Center)<br />
<br />
Richard Scheuermann (UTexas SW Medical Center at Dallas)<br />
<br />
Stuart Sealfon (Mount Sinai School of Medicine)<br />
<br />
Barry Smith (NCBO / University at Buffalo)<br />
<br />
Andrea Splendiani (Medical Informatics, Rennes, France)<br />
<br />
Balaji S. Srinivasan (Stanford University)<br />
<br />
Cathy Wu (Protein Ontology / PIR, Georgetown University)<br />
<br />
==Venue / Hotel Reservations ==<br />
<br />
[http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] <br />
<br />
Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make reservations either by calling 800-HILTONS and asking for the '''"National Center for Biomedical Ontology"''' block, or by entering group/convention code '''"NCB"''' when making reservations online at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] website. <br />
<br />
'''NOTE:''' To qualify for the special room block rate of $149 (+ tax) per night, reservations must be secured no later than '''Wednesday, March 5'''. After this date, reservations will be accepted based on availability and at prevailing rates.<br />
<br />
==Links ==<br />
<br />
* [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]<br />
<br />
==Literature==<br />
<br />
[http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]<br />
<br />
[http://xml.coverpages.org/OntologyExchange.html An evaluation of ontology exchange languages for bioinformatics]</div>Alanr