[Go-diff] GO update 08/01/2008

Fri Aug 1 21:30:46 PDT 2008

OBODIFF of gene_ontology_write.obo version 1.147 by 1.148

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034627
* Created object of type obo:TERM with id GO:0034628
* Created object of type obo:TERM with id GO:0034629
* Created object of type obo:TERM with id GO:0034630
* Created object of type obo:TERM with id GO:0034631
* Created object of type obo:TERM with id GO:0034632
* Created object of type obo:TERM with id GO:0034633
* Created object of type obo:TERM with id GO:0034634
* Created object of type obo:TERM with id GO:0034635
* Created object of type obo:TERM with id GO:0034636
* Populated new object GO:0034627 (macro)
  * Changed name of GO:0034627 from "<new term>" to "de novo NAD biosynthetic process"
  * Set definition of GO:0034627 to "The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of tryptophan or aspartate from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH."
  * Added definition dbxref GOC:imk to GO:0034627
  * Added definition dbxref PMID:17161604 to GO:0034627
  * Copied GO:0034627 to GO:0009435 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034627
* Populated new object GO:0034628 (macro)
  * Changed name of GO:0034628 from "<new term>" to "CLONE OF de novo NAD biosynthetic process from tryptophan"
  * Set definition of GO:0034628 to "The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of tryptophan from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH."
  * Added definition dbxref PMID:17161604 to GO:0034628
  * Copied GO:0034628 to GO:0034627 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034628
* Populated new object GO:0034629 (macro)
  * Changed name of GO:0034629 from "<new term>" to "cellular protein complex localization"
  * Set definition of GO:0034629 to "Any process by which a protein complex is transported to, or maintained in, a specific location within a cell."
  * Added definition dbxref GOC:mah to GO:0034629
  * Added synonym "establishment and maintenance of cellular protein complex localization" to GO:0034629
  * Changed synonym scope of GO:0034629 from "Related" to "Exact"
  * Copied GO:0034629 to GO:0031503 with type OBO_REL:is_a
  * Copied GO:0034629 to GO:0051641 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034629
* Populated new object GO:0034630 (macro)
  * Changed name of GO:0034630 from "<new term>" to "RITS complex localization"
  * Set definition of GO:0034630 to "Any process by which a RITS complex is transported to, or maintained in, a specific location."
  * Added definition dbxref GOC:mah to GO:0034630
  * Added synonym "establishment and maintenance of RITS complex localization" to GO:0034630
  * Changed synonym scope of GO:0034630 from "Related" to "Exact"
  * Copied GO:0034630 to GO:0034629 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034630
* Populated new object GO:0034631 (macro)
  * Changed name of GO:0034631 from "<new term>" to "microtubule anchoring at spindle pole body"
  * Set definition of GO:0034631 to "Any process by which a microtubule is maintained in a specific location in a cell by attachment to a spindle pole body. Microtubules attach to spindle pole bodies at the minus end."
  * Added definition dbxref GOC:mah to GO:0034631
  * Added definition dbxref PMID:17486116 to GO:0034631
  * Added synonym "attachment of spindle microtubules to SPB" to GO:0034631
  * Changed synonym scope of GO:0034631 from "Related" to "Exact"
  * Added synonym "attachment of spindle microtubules to spindle pole body" to GO:0034631
  * Changed synonym scope of GO:0034631 from "Related" to "Exact"
  * Added synonym "microtubule anchoring at SPB" to GO:0034631
  * Changed synonym scope of GO:0034631 from "Related" to "Exact"
  * Copied GO:0034631 to GO:0034453 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034631
* Populated new object GO:0034632 (macro)
  * Changed name of GO:0034632 from "<new term>" to "retinol transporter activity"
  * Set definition of GO:0034632 to "Enables the directed movement of retinol into, out of, within or between cells. Retinol is vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A."
  * Added definition dbxref GOC:mah to GO:0034632
  * Added definition dbxref GOC:vk to GO:0034632
  * Added synonym "vitamin A1 transporter activity" to GO:0034632
  * Changed synonym scope of GO:0034632 from "Related" to "Exact"
  * Copied GO:0034632 to GO:0051183 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034632
* Populated new object GO:0034633 (macro)
  * Changed name of GO:0034633 from "<new term>" to "retinol transport"
  * Set definition of GO:0034633 to "The directed movement of retinol into, out of, within or between cells. Retinol is vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A."
  * Added definition dbxref GOC:mah to GO:0034633
  * Added definition dbxref GOC:vk to GO:0034633
  * Added synonym "vitamin A1 transport" to GO:0034633
  * Changed synonym scope of GO:0034633 from "Related" to "Exact"
  * Copied GO:0034633 to GO:0051180 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034633
* Populated new object GO:0034634 (macro)
  * Changed name of GO:0034634 from "<new term>" to "glutathione transmembrane transporter activity"
  * Set definition of GO:0034634 to "Enables the directed movement of glutathione, the tripeptide glutamylcysteinylglycine, across a membrane into, out of, within or between cells."
  * Added definition dbxref GOC:mah to GO:0034634
  * Copied GO:0034634 to GO:0022891 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034634
* Populated new object GO:0034635 (macro)
  * Changed name of GO:0034635 from "<new term>" to "glutathione transport"
  * Set definition of GO:0034635 to "The directed movement of glutathione, the tripeptide glutamylcysteinylglycine, into, out of, within or between cells."
  * Added definition dbxref GOC:mah to GO:0034635
  * Copied GO:0034635 to GO:0042939 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034635
* Populated new object GO:0034636 (macro)
  * Changed name of GO:0034636 from "<new term>" to "strand invasion involved in gene conversion at mating-type locus"
  * Set definition of GO:0034636 to "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA at the mating-type locus. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules. This process occurs as part of gene conversion at the mating-type locus."
  * Added definition dbxref GOC:mah to GO:0034636
  * Added general dbxref Reactome:76004 to GO:0034636
  * Copied GO:0034636 to GO:0042148 with type OBO_REL:is_a
  * Copied GO:0034636 to GO:0007534 with type part_of
  * Assigned namespace "biological_process" to GO:0034636
* Added comment "This term was made obsolete because it is a grouping term that is not useful, but has caused true path violations."
* Changed definition of GO:0000051 from "The chemical reactions and pathways involving any of the intermediate compounds involved in the urea cycle, a cyclic metabolic pathway that converts waste nitrogen in the form of ammonium to urea." to "OBSOLETE. The chemical reactions and pathways involving any of the intermediate compounds involved in the urea cycle, a cyclic metabolic pathway that converts waste nitrogen in the form of ammonium to urea."
* Deleted GO:0000051 --part_of--> GO:0006807
* Deleted GO:0000051 --OBO_REL:is_a--> GO:0008152
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 106eae3
* Deleted GO:0000052 --OBO_REL:is_a--> GO:0000051
* Deleted GO:0000053 --OBO_REL:is_a--> GO:0000051
* Copied GO:0000053 to GO:0019794 with type OBO_REL:is_a
* Added synonym "ribosome export from cell nucleus" to GO:0000054
* Changed synonym scope of GO:0000054 from "Related" to "Exact"
* Added synonym "ribosomal large subunit export from cell nucleus" to GO:0000055
* Changed synonym scope of GO:0000055 from "Related" to "Exact"
* Added synonym "ribosomal small subunit export from cell nucleus" to GO:0000056
* Changed synonym scope of GO:0000056 from "Related" to "Exact"
* Added synonym "protein import into cell nucleus, translocation" to GO:0000060
* Changed synonym scope of GO:0000060 from "Related" to "Exact"
* Added synonym "protein import into cell nucleus, substrate release" to GO:0000061
* Changed synonym scope of GO:0000061 from "Related" to "Exact"
* Changed definition of GO:0000324 from "The vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure." to "A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure."
* Added definition dbxref GOC:mah to GO:0000324
* Added synonym "cell nucleus" to GO:0005634
* Changed synonym scope of GO:0005634 from "Related" to "Exact"
* Deleted GO:0005638 --part_of--> GO:0005637
* Deleted GO:0005732 --OBO_REL:is_a--> GO:0044424
* Added synonym "RNA import into cell nucleus" to GO:0006404
* Changed synonym scope of GO:0006404 from "Related" to "Exact"
* Added synonym "RNA export from cell nucleus" to GO:0006405
* Changed synonym scope of GO:0006405 from "Related" to "Exact"
* Added synonym "mRNA export from cell nucleus" to GO:0006406
* Changed synonym scope of GO:0006406 from "Related" to "Exact"
* Added synonym "rRNA export from cell nucleus" to GO:0006407
* Changed synonym scope of GO:0006407 from "Related" to "Exact"
* Added synonym "snRNA export from cell nucleus" to GO:0006408
* Changed synonym scope of GO:0006408 from "Related" to "Exact"
* Added synonym "tRNA export from cell nucleus" to GO:0006409
* Changed synonym scope of GO:0006409 from "Related" to "Exact"
* Deleted GO:0006412 --OBO_REL:is_a--> GO:0009059
* Copied GO:0006412 to GO:0043284 with type OBO_REL:is_a
* Deleted GO:0006525 --OBO_REL:is_a--> GO:0000051
* Deleted GO:0006591 --OBO_REL:is_a--> GO:0000051
* Added synonym "protein import into cell nucleus" to GO:0006606
* Changed synonym scope of GO:0006606 from "Related" to "Exact"
* Added synonym "NLS-bearing substrate import into cell nucleus" to GO:0006607
* Changed synonym scope of GO:0006607 from "Related" to "Exact"
* Added synonym "snRNP protein import into cell nucleus" to GO:0006608
* Changed synonym scope of GO:0006608 from "Related" to "Exact"
* Added synonym "mRNA-binding (hnRNP) protein import into cell nucleus" to GO:0006609
* Changed synonym scope of GO:0006609 from "Related" to "Exact"
* Added synonym "ribosomal protein import into cell nucleus" to GO:0006610
* Changed synonym scope of GO:0006610 from "Related" to "Exact"
* Added synonym "protein export from cell nucleus" to GO:0006611
* Changed synonym scope of GO:0006611 from "Related" to "Exact"
* Added synonym "microtubule anchoring at kinetochore" to GO:0008608
* Changed synonym scope of GO:0008608 from "Related" to "Exact"
* Deleted GO:0008608 --OBO_REL:is_a--> GO:0007017
* Copied GO:0008608 to GO:0034453 with type OBO_REL:is_a
* Deleted GO:0012508 --OBO_REL:is_a--> GO:0030660
* Deleted GO:0012509 --OBO_REL:is_a--> GO:0030660
* Deleted GO:0016567 --OBO_REL:is_a--> GO:0043687
* Copied GO:0016925 to GO:0043687 with type OBO_REL:is_a
* Added synonym "poly(A)+ mRNA export from cell nucleus" to GO:0016973
* Changed synonym scope of GO:0016973 from "Related" to "Exact"
* Copied GO:0019951 to GO:0043687 with type OBO_REL:is_a
* Deleted GO:0020017 --OBO_REL:is_a--> GO:0044459
* Copied GO:0030437 to GO:0022413 with type OBO_REL:is_a
* Added synonym "mitotic spindle organization and biogenesis in cell nucleus" to GO:0030472
* Changed synonym scope of GO:0030472 from "Related" to "Exact"
* Deleted GO:0030663 --OBO_REL:is_a--> GO:0044431
* Deleted GO:0030672 --OBO_REL:is_a--> GO:0044433
* Deleted GO:0031057 --OBO_REL:is_a--> GO:0051129
* Deleted GO:0031144 --OBO_REL:is_a--> GO:0031503
* Copied GO:0031144 to GO:0034629 with type OBO_REL:is_a
* Added synonym "mRNA export from cell nucleus during heat stress" to GO:0031990
* Changed synonym scope of GO:0031990 from "Related" to "Exact"
* Deleted GO:0032446 --OBO_REL:is_a--> GO:0043687
* Copied GO:0032446 to GO:0006464 with type OBO_REL:is_a
* Copied GO:0032447 to GO:0043687 with type OBO_REL:is_a
* Added synonym "regulation of protein import into cell nucleus, translocation" to GO:0033158
* Changed synonym scope of GO:0033158 from "Related" to "Exact"
* Added synonym "negative regulation of protein import into cell nucleus, translocation" to GO:0033159
* Changed synonym scope of GO:0033159 from "Related" to "Exact"
* Added synonym "positive regulation of protein import into cell nucleus, translocation" to GO:0033160
* Changed synonym scope of GO:0033160 from "Related" to "Exact"
* Added synonym "establishment and maintenance of gamma-tubulin complex localization" to GO:0033566
* Changed synonym scope of GO:0033566 from "Related" to "Exact"
* Deleted GO:0033566 --OBO_REL:is_a--> GO:0031503
* Copied GO:0033566 to GO:0034629 with type OBO_REL:is_a
* Changed name of GO:0034354 from "de novo NAD biosynthetic process" to "de novo NAD biosynthetic process from tryptophan"
* Deleted GO:0034354 --OBO_REL:is_a--> GO:0009435
* Copied GO:0034354 to GO:0034627 with type OBO_REL:is_a
* Added synonym "protein localization in cell nucleus" to GO:0034504
* Changed synonym scope of GO:0034504 from "Related" to "Exact"
* Deleted GO:0034620 --OBO_REL:is_a--> GO:0006950
* Deleted GO:0034620 --OBO_REL:is_a--> GO:0051789
* Added synonym "splicing factor protein import into nucleus" to GO:0035048
* Changed synonym scope of GO:0035048 from "Related" to "Exact"
* Added synonym "pre-microRNA export from cell nucleus" to GO:0035281
* Changed synonym scope of GO:0035281 from "Related" to "Exact"
* Added synonym "establishment of cell nucleus localization" to GO:0040023
* Changed synonym scope of GO:0040023 from "Related" to "Exact"
* Deleted GO:0042148 --part_of--> GO:0007534
* Added synonym "regulation of protein import into cell nucleus" to GO:0042306
* Changed synonym scope of GO:0042306 from "Related" to "Exact"
* Added synonym "positive regulation of protein import into cell nucleus" to GO:0042307
* Changed synonym scope of GO:0042307 from "Related" to "Exact"
* Added synonym "negative regulation of protein import into cell nucleus" to GO:0042308
* Changed synonym scope of GO:0042308 from "Related" to "Exact"
* Added synonym "regulation of NF-kappaB import into cell nucleus" to GO:0042345
* Changed synonym scope of GO:0042345 from "Related" to "Exact"
* Added synonym "positive regulation of NF-kappaB import into cell nucleus" to GO:0042346
* Changed synonym scope of GO:0042346 from "Related" to "Exact"
* Added synonym "negative regulation of NF-kappaB import into cell nucleus" to GO:0042347
* Changed synonym scope of GO:0042347 from "Related" to "Exact"
* Added synonym "NF-kappaB import into cell nucleus" to GO:0042348
* Changed synonym scope of GO:0042348 from "Related" to "Exact"
* Deleted GO:0042650 --OBO_REL:is_a--> GO:0044435
* Added synonym "regulation of transcription factor import into cell nucleus" to GO:0042990
* Changed synonym scope of GO:0042990 from "Related" to "Exact"
* Added synonym "transcription factor import into cell nucleus" to GO:0042991
* Changed synonym scope of GO:0042991 from "Related" to "Exact"
* Added synonym "negative regulation of transcription factor import into cell nucleus" to GO:0042992
* Changed synonym scope of GO:0042992 from "Related" to "Exact"
* Added synonym "positive regulation of transcription factor import into cell nucleus" to GO:0042993
* Changed synonym scope of GO:0042993 from "Related" to "Exact"
* Deleted GO:0043679 --OBO_REL:is_a--> GO:0044463
* Copied GO:0045116 to GO:0043687 with type OBO_REL:is_a
* Added synonym "MAPK export from cell nucleus" to GO:0045204
* Changed synonym scope of GO:0045204 from "Related" to "Exact"
* Added synonym "MAPK phosphatase export from cell nucleus" to GO:0045208
* Changed synonym scope of GO:0045208 from "Related" to "Exact"
* Added synonym "MAPK phosphatase export from cell nucleus, leptomycin B sensitive" to GO:0045209
* Changed synonym scope of GO:0045209 from "Related" to "Exact"
* Added synonym "intronless viral mRNA export from host cell nucleus" to GO:0046784
* Changed synonym scope of GO:0046784 from "Related" to "Exact"
* Added synonym "regulation of protein export from cell nucleus" to GO:0046825
* Changed synonym scope of GO:0046825 from "Related" to "Exact"
* Added synonym "negative regulation of protein export from cell nucleus" to GO:0046826
* Changed synonym scope of GO:0046826 from "Related" to "Exact"
* Added synonym "positive regulation of protein export from cell nucleus" to GO:0046827
* Changed synonym scope of GO:0046827 from "Related" to "Exact"
* Added synonym "regulation of RNA import into cell nucleus" to GO:0046828
* Changed synonym scope of GO:0046828 from "Related" to "Exact"
* Added synonym "negative regulation of RNA import into cell nucleus" to GO:0046829
* Changed synonym scope of GO:0046829 from "Related" to "Exact"
* Added synonym "positive regulation of RNA import into cell nucleus" to GO:0046830
* Changed synonym scope of GO:0046830 from "Related" to "Exact"
* Added synonym "regulation of RNA export from cell nucleus" to GO:0046831
* Changed synonym scope of GO:0046831 from "Related" to "Exact"
* Added synonym "negative regulation of RNA export from cell nucleus" to GO:0046832
* Changed synonym scope of GO:0046832 from "Related" to "Exact"
* Added synonym "positive regulation of RNA export from cell nucleus" to GO:0046833
* Changed synonym scope of GO:0046833 from "Related" to "Exact"
* Added synonym "cell nucleus inheritance" to GO:0048310
* Changed synonym scope of GO:0048310 from "Related" to "Exact"
* Deleted GO:0048701 --OBO_REL:is_a--> GO:0009653
* Added synonym "maintenance of protein location in cell nucleus" to GO:0051457
* Changed synonym scope of GO:0051457 from "Related" to "Exact"
* Added synonym "NFAT protein import into cell nucleus" to GO:0051531
* Changed synonym scope of GO:0051531 from "Related" to "Exact"
* Added synonym "regulation of NFAT protein import into cell nucleus" to GO:0051532
* Changed synonym scope of GO:0051532 from "Related" to "Exact"
* Added synonym "positive regulation of NFAT protein import into cell nucleus" to GO:0051533
* Changed synonym scope of GO:0051533 from "Related" to "Exact"
* Added synonym "negative regulation of NFAT protein import into cell nucleus" to GO:0051534
* Changed synonym scope of GO:0051534 from "Related" to "Exact"
* Deleted GO:0051601 --OBO_REL:is_a--> GO:0031503
* Copied GO:0051601 to GO:0034629 with type OBO_REL:is_a
* Added synonym "cell nucleus localization" to GO:0051647
* Changed synonym scope of GO:0051647 from "Related" to "Exact"
* Added synonym "maintenance of cell nucleus location" to GO:0051658
* Changed synonym scope of GO:0051658 from "Related" to "Exact"
* Deleted GO:0051664 --OBO_REL:is_a--> GO:0031503
* Copied GO:0051664 to GO:0034629 with type OBO_REL:is_a