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[Obo-diffs] changes for: ro_proposed
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From: <cj...@fr...> - 2007-10-27 11:10:46
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* Created object of type obo:TYPE with id OBO_REL:role_of * Created object of type obo:TYPE with id OBO_REL:towards * Created object of type obo:TYPE with id OBO_REL:has_phenotype * Created object of type obo:TYPE with id OBO_REL:relationship * Created object of type obo:TYPE with id OBO_REL:multiply_inheres_in * Created object of type obo:TYPE with id OBO_REL:occurs_with * Created object of type obo:TYPE with id OBO_REL:contains_variant_of * Populated new object OBO_REL:role_of (macro) * Changed name of OBO_REL:role_of from "OBO_REL:role_of" to "role_of" * Added comment "Example: 'to blood pump' function_of 'heart'" * added secondary id OBO_REL:0000032 to OBO_REL:role_of * Set definition of OBO_REL:role_of to "A relation between a role R and a= n entity E. R role_of E iff: R inheres_in E and R is a role" * Added definition dbxref GOC:cjm to OBO_REL:role_of * Created link OBO_REL:role_of -inverse_of-> OBO_REL:has_function * Created link OBO_REL:role_of -OBO_REL:is_a-> OBO_REL:inheres_in * Assigned namespace "relationship" to OBO_REL:role_of * Populated new object OBO_REL:towards (macro) * Changed name of OBO_REL:towards from "OBO_REL:towards" to "towards" * Added comment "Examples: sensitivity towards chlorine; the PATO:concent= ration of a liquid with respect to some chemical entity type" * added secondary id OBO_REL:0000036 to OBO_REL:towards * Set definition of OBO_REL:towards to "A relation between a relational q= uality and an entity type. Q towards E iff: for any qQt, q towards E at t. " * Added definition dbxref GOC:cjm to OBO_REL:towards * Added synonym "with respect to" to OBO_REL:towards * Added synonym "directed to" to OBO_REL:towards * Added synonym "to" to OBO_REL:towards * Added synonym "depends_on" to OBO_REL:towards * Assigned namespace "relationship" to OBO_REL:towards * Populated new object OBO_REL:has_phenotype (macro) * Changed name of OBO_REL:has_phenotype from "OBO_REL:has_phenotype" to "= has_phenotype" * Added comment "Human has_phenotype shape-of-skull; Spider has_phenotype= structure-of-web" * added secondary id OBO_REL:0000037 to OBO_REL:has_phenotype * Set definition of OBO_REL:has_phenotype to "A relation between an organ= ism and a quality or collection of qualities. Instance level: c has_phenoty= pe q iff: exists t such that c has_part_or_derivative p at t and p has_qual= ity q at t. For types: C has_phenotype Q iff: for any cCt, exists qQt such = that q inheres_in c at t. Here, c has_part_or_derivative p at t means that = c has_part(reflexive) p at t, or p derives_from c or some part_of c, or p a= rises through the actions of c" * Added definition dbxref GOC:cjm to OBO_REL:has_phenotype * Assigned namespace "relationship" to OBO_REL:has_phenotype * Populated new object OBO_REL:relationship (macro) * Changed name of OBO_REL:relationship from "OBO_REL:relationship" to "re= lationship" * Added comment "this relation was superfluous, so it has been obsoleted" * Set definition of OBO_REL:relationship to "A relationship between two c= lasses (terms). Relationships between classes are expressed in terms of rel= ations on underlying instances." * Added definition dbxref GOC:cjm to OBO_REL:relationship * org.geneontology.oboedit.history.ObsoleteObjectHistoryItem@4a0c68c3 * Assigned namespace "relationship" to OBO_REL:relationship * Populated new object OBO_REL:multiply_inheres_in (macro) * Changed name of OBO_REL:multiply_inheres_in from "OBO_REL:multiply_inhe= res_in" to "multiply_inheres_in" * added secondary id OBO_REL:generically_inheres_in to OBO_REL:multiply_i= nheres_in * Created link OBO_REL:multiply_inheres_in -OBO_REL:is_a-> OBO_REL:inhere= s_in * Assigned namespace "relationship" to OBO_REL:multiply_inheres_in * Populated new object OBO_REL:occurs_with (macro) * Changed name of OBO_REL:occurs_with from "OBO_REL:occurs_with" to "occu= rs_with" * Added comment "merge with OBO_REL:influences?" * Assigned namespace "relationship" to OBO_REL:occurs_with * Populated new object OBO_REL:contains_variant_of (macro) * Changed name of OBO_REL:contains_variant_of from "OBO_REL:contains_vari= ant_of" to "variant_of" * Added comment "merge with variant_of?" * Assigned namespace "relationship" to OBO_REL:contains_variant_of * Changed comment from "This relation links qualities, functions, dispositi= ons and other dependent continuants to their bearers. Example: A particular= shape that inheres in a lung; The redness that ineres in a Drosophila eye;= Catalytic activity inheres_in catalytic molecule" to "This relation links = qualities, functions, dispositions and other dependent continuants to their= bearers. Examples: A particular shape that inheres in a lung; The redness = that ineres in a Drosophila eye; Catalytic activity function inheres_in cat= alytic molecule. Note that inherence is a functional relation: if x inheres= _in y at t and x inheres_in z at t, then y=3Dz. We leave open the possibili= ty of a relation multiply_inheres_in, such as between a gene sequence and t= he multiple chromosomes it multiply inheres in. The super-relation of both = inheres_in and multiply_inheres_in would be depends_on" * added secondary id OBO_REL:0000026 to OBO_REL:inheres_in * Changed definition of OBO_REL:inheres_in from "A relation between a depen= dent continuant and an entity. D inheres_in E iff: any any dDt, exists eEt = such that d inheres_in e at t" to "A relation between a dependent continuan= t D and an entity E. D inheres_in E iff: given any d that instantiates D at= t, there exists some e that instantiates E at t and d *inheres_in* e at t.= Here *inheres_in* is the primitive instance level relation." * Added definition dbxref GOC:cjm to OBO_REL:inheres_in * added secondary id OBO_REL:0000027 to OBO_REL:bearer_of * Changed definition of OBO_REL:bearer_of from "A relation between an entit= y and a dependent continuant" to "A relation between an entity and a depend= ent continuant; the reciprocal relation of inheres_in" * Added definition dbxref GOC:cjm to OBO_REL:bearer_of * Added synonym "has_inherer" to OBO_REL:bearer_of * Changed synonym scope of OBO_REL:bearer_of from "Related" to "Exact" * Destroyed object OBO_REL:generically_inheres_in * Created link OBO_REL:specifically_inheres_in -OBO_REL:is_a-> OBO_REL:inhe= res_in * org.geneontology.oboedit.history.ObsoleteObjectHistoryItem@74b2002f * added secondary id OBO_REL:0000028 to OBO_REL:quality_of * Changed definition of OBO_REL:quality_of from "As inheres_in, where the d= ependent continuant is specifically a quality" to "A relation between a qua= lity Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quali= ty" * Added definition dbxref GOC:cjm to OBO_REL:quality_of * Added synonym "is_quality_of" to OBO_REL:quality_of * Changed synonym scope of OBO_REL:quality_of from "Related" to "Exact" * added secondary id OBO_REL:has_quality to OBO_REL:has_quality * added secondary id OBO_REL:0000029 to OBO_REL:has_quality * Added definition dbxref GOC:cjm to OBO_REL:has_quality * Created link OBO_REL:has_quality -OBO_REL:is_a-> OBO_REL:bearer_of * Changed comment from "get def from CARO chapter" to "Examples: eye develo= ps_from eye disc; erythrocyte develops_from reticulocyte. Note that ontolog= ies should use either derives_from or transformation_of where appropriate, = but the develops_from relation can be used where one does not want to diffe= rentiate between these 2 cases" * added secondary id OBO_REL:0000038 to OBO_REL:develops_from * Set definition of OBO_REL:develops_from to "A relation between two contin= uants, C and D. C develops_from D if C derived_from D or C transformation_o= f D. On the class level: C develops from D if and only if, for any x and an= y time t, the following holds: if x instantiates C at time t, then 1. eithe= r for some time t1, x instantiates D at t1 and t1 precedes t, and there is = no time interval t2 such that x instantiates C at t2 and x instantiates D a= t t2 ; 2. or for some time t1 , there is some y such that y instantiates D = at t1 and x derived_from y. On the instance level: x develops_from y is ind= istinguishable from x derives_from y" * Added definition dbxref GOC:cjm to OBO_REL:develops_from * changed "is transitive" status of OBO_REL:develops_from to true * added secondary id OBO_REL:0000031 to OBO_REL:has_function * Added definition dbxref GOC:cjm to OBO_REL:has_function * Created link OBO_REL:has_function -OBO_REL:is_a-> OBO_REL:bearer_of * Changed comment from "the function of "blood pump" function_of "heart"" t= o "Example: 'to blood pump' function_of 'heart'" * added secondary id OBO_REL:0000030 to OBO_REL:function_of * Changed definition of OBO_REL:function_of from "Relation between a functi= on and an independent continuant" to "A relation between a function F and a= n entity E. F function_of E iff: Q inheres_in E and Q is a function" * Added definition dbxref GOC:cjm to OBO_REL:function_of * Created link OBO_REL:function_of -OBO_REL:is_a-> OBO_REL:inheres_in * Changed comment from "The process of 'histidine catabolism' (GO:0006548) = realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note= : here 'activity' denotes a function and not a process)." to "The process o= f 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammo= nia lyase activity' (GO:0004397) (note: here 'activity' denotes a function = and not a process). We leave open the possibility of defining in future the= sub-relations directly_realizes (as bewteen a function and it's functionin= g) and indirectly_realizes" * added secondary id OBO_REL:0000034 to OBO_REL:realizes * Changed definition of OBO_REL:realizes from "Relation between a process a= nd a function. p executes f: exists Continuant c, Time t such that c partic= ipates_in p at t, c executes f at t. Type: all pP, exists fFt such that p e= xecutes f" to "Relation between a process and a function, where the unfoldi= ng of the process requires the execution of the function. Class level: P re= alizes F iff: given any p that instantiates P, there exists some f, t such = that f instantiates F at t and p *realizes* f. Here, *realizes* is the prim= itive instance level relation" * Added definition dbxref GOC:cjm to OBO_REL:realizes * added secondary id OBO_REL:0000035 to OBO_REL:realized_by * Set definition of OBO_REL:realized_by to "Relation between a function and= a process. Reciprocal relation of realizes" * Added definition dbxref GOC:cjm to OBO_REL:realized_by * added secondary id OBO_REL:0000033 to OBO_REL:has_role * Set definition of OBO_REL:has_role to "A relation between a continuant C = and a role R. The reciprocal relation of role_of." * Added definition dbxref GOC:cjm to OBO_REL:has_role * Created link OBO_REL:has_role -OBO_REL:is_a-> OBO_REL:bearer_of * Added comment "do we use the same relation between processes as between c= ontinuants? For example, proteinX participates_in P1 that regulates P2; vs = X regulates P2." |