[Go-diff] GO update 07/07/2009

Tue Jul 7 21:30:58 PDT 2009

OBODIFF of gene_ontology_write.obo version 1.697 by 1.698

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0070783
* Created object of type obo:TERM with id GO:0070784
* Created object of type obo:TERM with id GO:0070785
* Created object of type obo:TERM with id GO:0070786
* Populated new object GO:0070783 (macro)
  * Changed name of GO:0070783 from "<new term>" to "growth of unicellular organism as a thread of attached cells"
  * Set definition of GO:0070783 to "A filamentous growth process in which cells remain attached after division and form thread-like filaments that may penetrate into a solid growth medium such as an agar plate, exhibited by unicellular fungi under certain growth conditions."
  * Added definition dbxref GOC:mah to GO:0070783
  * Added definition dbxref GOC:mcc to GO:0070783
  * Added GO:0070783 to category goslim_candida
  * Copied GO:0070783 to GO:0030447 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070783
* Populated new object GO:0070784 (macro)
  * Changed name of GO:0070784 from "<new term>" to "regulation of growth of unicellular organism as a thread of attached cells"
  * Set definition of GO:0070784 to "Any process that modulates the frequency, rate or extent of the process in which cells remain attached after division and form thread-like filaments that may penetrate into a solid growth medium."
  * Added definition dbxref GOC:mah to GO:0070784
  * Copied GO:0070784 to GO:0010570 with type OBO_REL:is_a
  * Copied GO:0070784 to GO:0070783 with type regulates
  * Assigned namespace "biological_process" to GO:0070784
* Populated new object GO:0070785 (macro)
  * Changed name of GO:0070785 from "<new term>" to "negative regulation of growth of unicellular organism as a thread of attached cells"
  * Set definition of GO:0070785 to "Any process that decreases the frequency, rate or extent of the process in which cells remain attached after division and form thread-like filaments that may penetrate into a solid growth medium."
  * Added definition dbxref GOC:mah to GO:0070785
  * Copied GO:0070785 to GO:0060258 with type OBO_REL:is_a
  * Copied GO:0070785 to GO:0070783 with type negatively_regulates
  * Copied GO:0070785 to GO:0070784 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070785
* Populated new object GO:0070786 (macro)
  * Changed name of GO:0070786 from "<new term>" to "positive regulation of growth of unicellular organism as a thread of attached cells"
  * Set definition of GO:0070786 to "Any process that activates or increases the frequency, rate or extent of the process in which cells remain attached after division and form thread-like filaments that may penetrate into a solid growth medium."
  * Added definition dbxref GOC:mah to GO:0070786
  * Copied GO:0070786 to GO:0070784 with type OBO_REL:is_a
  * Copied GO:0070786 to GO:0070783 with type positively_regulates
  * Copied GO:0070786 to GO:0045927 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070786
* Copied GO:0000052 to GO:0006575 with type OBO_REL:is_a
* Deleted synonym "actomyosin ring" from GO:0000142
* Deleted synonym "contractile ring" from GO:0000142
* Deleted synonym "cytokinetic ring" from GO:0000142
* Deleted synonym "septin ring" from GO:0000144
* Deleted synonym "hydrogen-transporting ATP synthase, stator stalk" from GO:0000274
* Deleted synonym "proton-transporting ATP synthase, stator stalk" from GO:0000274
* Deleted synonym "hydrogen-transporting ATP synthase, F0 sector" from GO:0000276
* Deleted synonym "proton-transporting ATP synthase complex, coupling factor F(0)" from GO:0000276
* Deleted synonym "proton-transporting ATP synthase complex, coupling factor F(o)" from GO:0000276
* Deleted synonym "conjugation" from GO:0000747
* Deleted GO:0001403 --OBO_REL:is_a--> GO:0030447
* Copied GO:0001403 to GO:0070783 with type OBO_REL:is_a
* Deleted synonym "optic placode formation" from GO:0001744
* Deleted synonym "down regulation of adaptive immune response" from GO:0002823
* Deleted synonym "down-regulation of adaptive immune response" from GO:0002823
* Deleted synonym "downregulation of adaptive immune response" from GO:0002823
* Deleted synonym "inhibition of adaptive immune response" from GO:0002823
* Deleted synonym "activation of adaptive immune response" from GO:0002824
* Deleted synonym "positive regulation of adaptive immune response" from GO:0002824
* Deleted synonym "stimulation of adaptive immune response" from GO:0002824
* Deleted synonym "up regulation of adaptive immune response" from GO:0002824
* Deleted synonym "up-regulation of adaptive immune response" from GO:0002824
* Deleted synonym "upregulation of adaptive immune response" from GO:0002824
* Changed synonym scope of GO:0005213 from "Exact" to "Narrow"
* Deleted synonym "structural constituent of cuticle" from GO:0005214
* Deleted synonym "NADH dehydrogenase complex (ubiquinone)" from GO:0005747
* Deleted synonym "respiratory chain complex I" from GO:0005747
* Deleted synonym "fumarate reductase complex" from GO:0005749
* Deleted synonym "respiratory chain complex II" from GO:0005749
* Deleted synonym "succinate dehydrogenase complex" from GO:0005749
* Deleted synonym "succinate dehydrogenase complex (ubiquinone)" from GO:0005749
* Deleted synonym "respiratory chain complex III" from GO:0005750
* Deleted synonym "ubiquinol-cytochrome c oxidoreductase complex" from GO:0005750
* Deleted synonym "ubiquinol-cytochrome-c reductase complex" from GO:0005750
* Deleted synonym "cytochrome c oxidase complex" from GO:0005751
* Deleted synonym "respiratory chain complex IV" from GO:0005751
* Deleted synonym "hydrogen-translocating F-type ATPase complex" from GO:0005753
* Deleted synonym "hydrogen-transporting ATP synthase" from GO:0005753
* Deleted synonym "proton-transporting ATP synthase complex" from GO:0005753
* Deleted synonym "respiratory chain complex V" from GO:0005753
* Added synonym "mitochondrial respiratory chain complex V" to GO:0005753
* Changed synonym scope of GO:0005753 from "Related" to "Exact"
* Deleted synonym "hydrogen-transporting ATP synthase, catalytic core" from GO:0005754
* Deleted synonym "proton-transporting ATP synthase, catalytic core" from GO:0005754
* Deleted synonym "hydrogen-transporting ATP synthase, central stalk" from GO:0005756
* Deleted synonym "proton-transporting ATP synthase, central stalk" from GO:0005756
* Added synonym "cytokinetic ring" to GO:0005826
* Changed synonym scope of GO:0005826 from "Related" to "Exact"
* Added synonym "cellular modified amino acid metabolic process" to GO:0006575
* Added general dbxref ChEBI:25359 to synonym cellular modified amino acid metabolic process of GO:0006575
* Added general dbxref GOC:mah to synonym cellular modified amino acid metabolic process of GO:0006575
* Changed synonym scope of GO:0006575 from "Related" to "Exact"
* Deleted GO:0007124 --OBO_REL:is_a--> GO:0030447
* Copied GO:0007124 to GO:0070783 with type OBO_REL:is_a
* Copied GO:0009116 to GO:0046483 with type OBO_REL:is_a
* Copied GO:0009164 to GO:0046700 with type OBO_REL:is_a
* Copied GO:0009394 to GO:0019692 with type OBO_REL:is_a
* Deleted GO:0010322 --OBO_REL:is_a--> GO:0010675
* Deleted GO:0010337 --OBO_REL:is_a--> GO:0031323
* Copied GO:0016259 to GO:0006575 with type OBO_REL:is_a
* Copied GO:0016261 to GO:0042219 with type OBO_REL:is_a
* Deleted GO:0016585 --OBO_REL:is_a--> GO:0044451
* Copied GO:0016585 to GO:0044428 with type OBO_REL:is_a
* Changed comment from "Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function possessed by this complex is represented by the molecular function term 'ferredoxin:thioredoxin reductase activity ; GO:0030385'. Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the relationship: only_in_taxon NCBITaxon:33090" to "Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function possessed by this complex is represented by the molecular function term 'ferredoxin:thioredoxin reductase activity ; GO:0030385'."
* Copied GO:0030869 to GO:0044452 with type OBO_REL:is_a
* Changed definition of GO:0032133 from "A eukaryotically conserved protein complex that localizes to kinetochores in early mitosis, the spindle mid-zone in anaphase B and to the telophase midbody. It has been proposed that the passenger complex coordinates various events based on its location to different structures during the course of mitosis. Complex members include the BIR-domain containing protein survivin, aurora kinase and INCENP." to "A eukaryotically conserved protein complex that localizes to kinetochores in early mitosis, the spindle mid-zone in anaphase B and to the telophase midbody. It has been proposed that the passenger complex coordinates various events based on its location to different structures during the course of mitosis. Complex members include the BIR-domain-containing protein Survivin, Aurora B kinase, INCENP and Borealin."
* Added definition dbxref PMID:19570910 to GO:0032133
* Deleted GO:0033247 --OBO_REL:is_a--> GO:0031329
* Deleted GO:0033249 --OBO_REL:is_a--> GO:0031331
* Added synonym "hydrogen-transporting ATP synthase complex, coupling factor F(o)" to GO:0045263
* Added general dbxref GOC:mah to synonym hydrogen-transporting ATP synthase complex, coupling factor F(o) of GO:0045263
* Changed synonym scope of GO:0045263 from "Related" to "Exact"
* Deleted GO:0045853 --OBO_REL:is_a--> GO:0048519
* Deleted GO:0045854 --OBO_REL:is_a--> GO:0048518
* Deleted GO:0046499 --OBO_REL:is_a--> GO:0046483
* Deleted GO:0046500 --OBO_REL:is_a--> GO:0046483
* Changed definition of GO:0070187 from "A nuclear telomere cap complex that is formed by the association of the shelterin protein (POT1 or a homolog thereof) and several other proteins with telomeric DNA. The complex contains TRF1, TRF2, POT1, RAP1, TIN2 and TPP1 in mammalian cells, and Pot1, Tpz1, Ccq1, Poz1, and Rap1 in Schizosaccharomyces." to "A nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase. The complex contains TRF1, TRF2, POT1, RAP1, TIN2 and TPP1 in mammalian cells, and Pot1, Tpz1, Ccq1, Poz1, and Rap1 in Schizosaccharomyces. Taz1 and Rap1 (or their mammalian equivalents) form a dsDNA-binding subcomplex, Pot1 and Tpz1 form an ssDNA-binding subcomplex, and the two subcomplexes are bridged by Poz1."
* Added definition dbxref GOC:expert_mf to GO:0070187