part_of part of BFO:0000050 part_of Intended meaning: Ambiguous between continuant-parthood and occurrent-parthood. domain: continuant range: continuant time: at some time domain: occurrent range: occurrent time: atemporal Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. http://www.obofoundry.org/ro/#OBO_REL:part_of part of part_of has part has_part has part BFO:0000051 has_part has_part Intended meaning: Ambiguous between continuant-parthood and occurrent-parthood. domain: continuant range: continuant time: at some time domain: occurrent range: occurrent time: atemporal has part has_part overlaps overlaps x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) temporally related to https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. starts Allen Chris Mungall inverse of starts with starts with Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. started by ends inverse of ends with ends with finished by x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. mereotopologically related to Chris Mungall A mereological relationship or a topological relationship entity entity occurrent An entity that has temporal parts and that happens, unfolds or develops through time. a surgical operation as processual context for a nosocomical infection occurrent perdurant the life of an organism the most interesting part of Van Gogh's life the spatiotemporal context occupied by a process of cellular meiosis the spatiotemporal region occupied by the development of a cancer tumor molecular_function nucleic acid binding DNA binding DNA replication origin binding catalytic activity DNA-directed DNA polymerase activity DNA primase activity DNA-directed RNA polymerase activity DNA ligase activity nuclease activity endonuclease activity endoribonuclease activity RNA-DNA hybrid ribonuclease activity exonuclease activity ribonuclease activity binding nucleobase-containing compound metabolic process DNA metabolic process DNA replication DNA-dependent DNA replication DNA ligation DNA unwinding involved in DNA replication DNA replication, synthesis of RNA primer DNA replication initiation DNA strand elongation involved in DNA replication leading strand elongation lagging strand elongation DNA replication termination RNA catabolic process cellular aromatic compound metabolic process nitrogen compound metabolic process biological_process metabolic process catabolic process macromolecule catabolic process biosynthetic process macromolecule biosynthetic process cellular process cellular component organization RNA metabolic process transferase activity transferase activity, transferring phosphorus-containing groups nucleotidyltransferase activity hydrolase activity hydrolase activity, acting on ester bonds ligase activity ligase activity, forming phosphoric ester bonds endoribonuclease activity, producing 5'-phosphomonoesters endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters heterocycle biosynthetic process aromatic compound biosynthetic process aromatic compound catabolic process cellular component assembly DNA strand elongation DNA geometric change DNA duplex unwinding RNA biosynthetic process DNA replication, Okazaki fragment processing DNA polymerase activity RNA polymerase activity cellular macromolecular complex assembly cellular nitrogen compound metabolic process cellular macromolecule biosynthetic process nucleobase-containing compound biosynthetic process nucleobase-containing compound catabolic process pre-replicative complex assembly DNA replication, removal of RNA primer macromolecule metabolic process sequence-specific DNA binding macromolecular complex subunit organization cellular component biogenesis cellular metabolic process primary metabolic process cellular catabolic process cellular biosynthetic process cellular macromolecule metabolic process cellular macromolecule catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound biosynthetic process heterocycle metabolic process heterocycle catabolic process DNA ligation involved in DNA-dependent DNA replication macromolecular complex assembly protein-DNA complex assembly DNA conformation change organic substance metabolic process protein-DNA complex subunit organization cellular component organization or biogenesis DNA biosynthetic process nucleic acid metabolic process nucleic acid phosphodiester bond hydrolysis RNA phosphodiester bond hydrolysis RNA phosphodiester bond hydrolysis, endonucleolytic organic cyclic compound binding organic cyclic compound metabolic process organic cyclic compound catabolic process organic cyclic compound biosynthetic process heterocyclic compound binding organic substance catabolic process organic substance biosynthetic process SPAC12B10.15c rfc4 cdc45 dpb3 cdt2 mcm5 rtf2 cdc17 fml2 psf3 rfc2 sld3 SPAC26H5.02c cdc1 rfc3 rim1 pol4 rqh1 rad2 orc3 pol1 rnh201 slx4 rev3 spp1 drc1 cdc24 fml1 mcl1 cbp1 cdm1 rev7 rev1 SPBC1347.08c cdc23 cdc18 pol5 eso1 dna2 pcn1 top3 cdc27 spp2 abp2 top2 mcm6 rfc1 mcm7 cdc20 orc1 orc6 cdc6 SPBC365.09c dpb4 mcm2 cdt1 orc5 ssb1 orc2 psf2 hsk1 rfc5 ibp1 noc3 pfh1 elg1 psf1 orc4 sld5 dpb2 mcm3 mcm4 SPCC16C4.22 ssb2 ssb3 pog1 kpa1 spb70 SPCC737.07c molecular_function enabled by SPBC365.09c (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by SPCC737.07c (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by cbp1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by cdc18 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by cdc24 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by cdc45 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by cdt1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by cdt2 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by drc1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by elg1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by fml1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by fml2 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by hsk1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by ibp1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by mcl1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by mcm4 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by mcm6 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by mcm7 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by noc3 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by psf1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by psf2 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by psf3 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by rfc1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by rfc2 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by rfc3 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by rfc4 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by rfc5 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by rim1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by rtf2 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by sld3 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by sld5 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by ssb1 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by ssb2 (pVal_uncorrected=null, p(F|P)=1.0) molecular_function enabled by ssb3 (pVal_uncorrected=null, p(F|P)=1.0) DNA binding enabled by rad2 (pVal_uncorrected=3.204943078971567E-5, p(F|P)=0.4545454545454546) DNA binding enabled by SPAC26H5.02c (pVal_uncorrected=7.363041791830227E-6, p(F|P)=0.42857142857142855) DNA binding enabled by cdc17 (pVal_uncorrected=3.204943078971567E-5, p(F|P)=0.09090909090909091) DNA binding enabled by cdc20 (pVal_uncorrected=6.039613253960852E-14, p(F|P)=0.48387096774193544) DNA binding enabled by dpb2 (pVal_uncorrected=6.039613253960852E-14, p(F|P)=0.48387096774193544) DNA binding enabled by mcm2 (pVal_uncorrected=6.039613253960852E-14, p(F|P)=0.48387096774193544) DNA binding enabled by mcm3 (pVal_uncorrected=6.039613253960852E-14, p(F|P)=0.48387096774193544) DNA binding enabled by mcm5 (pVal_uncorrected=6.039613253960852E-14, p(F|P)=0.48387096774193544) DNA binding enabled by pcn1 (pVal_uncorrected=1.336036942301E-6, p(F|P)=0.34782608695652173) DNA binding enabled by pfh1 (pVal_uncorrected=3.204943078971567E-5, p(F|P)=0.4545454545454546) DNA binding enabled by pol4 (pVal_uncorrected=6.539213615042172E-14, p(F|P)=0.050632911392405056) DNA binding enabled by rqh1 (pVal_uncorrected=0.038811513463323566, p(F|P)=1.0) DNA binding enabled by spb70 (pVal_uncorrected=6.039613253960852E-14, p(F|P)=0.48387096774193544) DNA binding enabled by top2 (pVal_uncorrected=1.336036942301E-6, p(F|P)=0.34782608695652173) DNA binding enabled by top3 (pVal_uncorrected=6.039613253960852E-14, p(F|P)=0.4) DNA replication origin binding enabled by abp2 (pVal_uncorrected=-1.9761969838327786E-14, p(F|P)=0.25806451612903225) DNA replication origin binding enabled by orc1 (pVal_uncorrected=-1.9761969838327786E-14, p(F|P)=0.25806451612903225) DNA replication origin binding enabled by orc2 (pVal_uncorrected=-1.9761969838327786E-14, p(F|P)=0.25806451612903225) DNA replication origin binding enabled by orc3 (pVal_uncorrected=-1.9761969838327786E-14, p(F|P)=0.25806451612903225) DNA replication origin binding enabled by orc4 (pVal_uncorrected=-1.9761969838327786E-14, p(F|P)=0.25806451612903225) DNA replication origin binding enabled by orc5 (pVal_uncorrected=-1.9761969838327786E-14, p(F|P)=0.25806451612903225) DNA replication origin binding enabled by orc6 (pVal_uncorrected=-1.9761969838327786E-14, p(F|P)=0.25806451612903225) DNA replication origin binding enabled by pol1 (pVal_uncorrected=-1.9761969838327786E-14, p(F|P)=0.16129032258064516) sequence-specific DNA binding enabled by dpb4 (pVal_uncorrected=-4.951594689828198E-14, p(F|P)=0.16129032258064516) DNA-directed DNA polymerase activity enabled by cdc1 (pVal_uncorrected=5.090259732165592E-6, p(F|P)=0.4545454545454546) DNA-directed DNA polymerase activity enabled by cdc27 (pVal_uncorrected=5.090259732165592E-6, p(F|P)=0.27272727272727276) DNA-directed DNA polymerase activity enabled by cdc6 (pVal_uncorrected=5.090259732165592E-6, p(F|P)=0.4545454545454546) DNA-directed DNA polymerase activity enabled by cdm1 (pVal_uncorrected=7.44147796050143E-7, p(F|P)=0.17391304347826086) DNA-directed DNA polymerase activity enabled by dpb3 (pVal_uncorrected=3.587130592563881E-13, p(F|P)=0.22784810126582278) DNA-directed DNA polymerase activity enabled by eso1 (pVal_uncorrected=0.0, p(F|P)=0.2) DNA-directed DNA polymerase activity enabled by kpa1 (pVal_uncorrected=0.0, p(F|P)=0.2) DNA-directed DNA polymerase activity enabled by pog1 (pVal_uncorrected=0.0, p(F|P)=0.4) DNA-directed DNA polymerase activity enabled by pol5 (pVal_uncorrected=0.0, p(F|P)=0.2) DNA-directed DNA polymerase activity enabled by rev1 (pVal_uncorrected=0.0, p(F|P)=0.2) DNA-directed DNA polymerase activity enabled by rev3 (pVal_uncorrected=0.0, p(F|P)=0.4) DNA-directed DNA polymerase activity enabled by rev7 (pVal_uncorrected=0.0, p(F|P)=0.2) DNA primase activity enabled by cdc23 (pVal_uncorrected=2.1528988591867915E-9, p(F|P)=0.043478260869565216) DNA primase activity enabled by spp1 (pVal_uncorrected=2.1528988591867915E-9, p(F|P)=0.37500000000000006) DNA primase activity enabled by spp2 (pVal_uncorrected=2.1528988591867915E-9, p(F|P)=0.37500000000000006) RNA-DNA hybrid ribonuclease activity enabled by SPAC12B10.15c (pVal_uncorrected=6.329233859236894E-8, p(F|P)=0.27272727272727276) RNA-DNA hybrid ribonuclease activity enabled by SPBC1347.08c (pVal_uncorrected=6.329233859236894E-8, p(F|P)=0.27272727272727276) RNA-DNA hybrid ribonuclease activity enabled by rnh201 (pVal_uncorrected=6.329233859236894E-8, p(F|P)=0.27272727272727276) endonuclease activity enabled by slx4 (pVal_uncorrected=2.144617816668415E-12, p(F|P)=0.2) exonuclease activity enabled by dna2 (pVal_uncorrected=0.010175679159289186, p(F|P)=0.09090909090909091) sequence-specific DNA binding enabled by SPCC16C4.22 (pVal_uncorrected=-4.951594689828198E-14, p(F|P)=0.0)