[Go-diff] GO update 08/13/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Wed Aug 13 21:30:47 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.162 by 1.164

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034646
* Created object of type obo:TERM with id GO:0034647
* Created object of type obo:TERM with id GO:0034648
* Created object of type obo:TERM with id GO:0034649
* Created object of type obo:TERM with id GO:0034650
* Created object of type obo:TERM with id GO:0034651
* Created object of type obo:TERM with id GO:0034652
* Created object of type obo:TERM with id GO:0034653
* Populated new object GO:0034646 (macro)
  * Changed name of GO:0034646 from "<new term>" to "organelle-enclosing lipid monolayer"
  * Set definition of GO:0034646 to "A lipid monolayer that surrounds and encloses an organelle."
  * Added definition dbxref GOC:mah to GO:0034646
  * Copied GO:0034646 to GO:0044446 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034646
* Populated new object GO:0034647 (macro)
  * Changed name of GO:0034647 from "<new term>" to "histone demethylase activity (H3-trimethyl-K4 specific)"
  * Set definition of GO:0034647 to "Catalysis of the removal of a methyl group from trimethylated lysine at position 4 of the histone H3 protein."
  * Added definition dbxref GOC:mah to GO:0034647
  * Added definition dbxref PMID:17550896 to GO:0034647
  * Added synonym "histone demethylase activity (H3-K4-me3 specific)" to GO:0034647
  * Changed synonym scope of GO:0034647 from "Related" to "Exact"
  * Copied GO:0034647 to GO:0032453 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034647
* Populated new object GO:0034648 (macro)
  * Changed name of GO:0034648 from "<new term>" to "histone demethylase activity (H3-dimethyl-K4 specific)"
  * Set definition of GO:0034648 to "Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein."
  * Added definition dbxref GOC:mah to GO:0034648
  * Added definition dbxref PMID:17550896 to GO:0034648
  * Added synonym "histone demethylase activity (H3-K4-me2 specific)" to GO:0034648
  * Changed synonym scope of GO:0034648 from "Related" to "Exact"
  * Copied GO:0034648 to GO:0032453 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034648
* Populated new object GO:0034649 (macro)
  * Changed name of GO:0034649 from "<new term>" to "histone demethylase activity (H3-monomethyl-K4 specific)"
  * Set definition of GO:0034649 to "Catalysis of the removal of a methyl group from monomethylated lysine at position 4 of the histone H3 protein."
  * Added definition dbxref GOC:mah to GO:0034649
  * Added definition dbxref PMID:17550896 to GO:0034649
  * Added synonym "histone demethylase activity (H3-K4-me1 specific)" to GO:0034649
  * Changed synonym scope of GO:0034649 from "Related" to "Exact"
  * Copied GO:0034649 to GO:0032453 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034649
* Populated new object GO:0034650 (macro)
  * Changed name of GO:0034650 from "<new term>" to "cortisol metabolic process"
  * Set definition of GO:0034650 to "The chemical reactions and pathways involving cortisol, the steroid hormone 11-beta-17,21-trihydroxypregn-4-ene-3,20-dione. Cortisol is synthesized from cholesterol in the adrenal gland and controls carbohydrate, fat and protein metabolism and has anti-inflammatory
properties."
  * Added definition dbxref ChEBI:17650 to GO:0034650
  * Added definition dbxref GOC:mah to GO:0034650
  * Added definition dbxref GOC:rl to GO:0034650
  * Added synonym "cortisol metabolism" to GO:0034650
  * Changed synonym scope of GO:0034650 from "Related" to "Exact"
  * Copied GO:0034650 to GO:0008207 with type OBO_REL:is_a
  * Copied GO:0034650 to GO:0008211 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034650
* Populated new object GO:0034651 (macro)
  * Changed name of GO:0034651 from "<new term>" to "cortisol biosynthetic process"
  * Set definition of GO:0034651 to "The chemical reactions and pathways resulting in the formation of cortisol, the steroid hormone 11-beta-17,21-trihydroxypregn-4-ene-3,20-dione. Cortisol is synthesized from cholesterol in the adrenal gland and controls carbohydrate, fat and protein metabolism and has anti-inflammatory
properties."
  * Added definition dbxref ChEBI:17650 to GO:0034651
  * Added definition dbxref GOC:mah to GO:0034651
  * Added definition dbxref GOC:rl to GO:0034651
  * Added synonym "cortisol anabolism" to GO:0034651
  * Changed synonym scope of GO:0034651 from "Related" to "Narrow"
  * Added synonym "cortisol biosynthesis" to GO:0034651
  * Changed synonym scope of GO:0034651 from "Related" to "Exact"
  * Added synonym "cortisol formation" to GO:0034651
  * Changed synonym scope of GO:0034651 from "Related" to "Exact"
  * Added synonym "cortisol synthesis" to GO:0034651
  * Changed synonym scope of GO:0034651 from "Related" to "Exact"
  * Copied GO:0034651 to GO:0006700 with type OBO_REL:is_a
  * Copied GO:0034651 to GO:0006704 with type OBO_REL:is_a
  * Copied GO:0034651 to GO:0034650 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034651
* Populated new object GO:0034652 (macro)
  * Changed name of GO:0034652 from "<new term>" to "extrachromosomal circular DNA localization during cell aging"
  * Added comment "Note that the term string was changed to be consistent with placement of this term in cell aging hierarchy."
  * Set definition of GO:0034652 to "Any process by which extrachromosomal circular DNA molecules are transported to, or maintained in, a specific location in cells as they age."
  * Added definition dbxref GOC:jp to GO:0034652
  * Added definition dbxref PMID:18660802 to GO:0034652
  * Added synonym "extrachromosomal circular DNA localisation during cell ageing" to GO:0034652
  * Changed synonym scope of GO:0034652 from "Related" to "Exact"
  * Copied GO:0034652 to GO:0001301 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034652
* Populated new object GO:0034653 (macro)
  * Changed name of GO:0034653 from "<new term>" to "retinoic acid catabolic process"
  * Set definition of GO:0034653 to "The chemical reactions and pathways resulting in the breakdown of retinoic acid, one of the three components that makes up vitamin A."
  * Added definition dbxref GOC:mah to GO:0034653
  * Added synonym "retinoic acid breakdown" to GO:0034653
  * Changed synonym scope of GO:0034653 from "Related" to "Exact"
  * Added synonym "retinoic acid catabolism" to GO:0034653
  * Changed synonym scope of GO:0034653 from "Related" to "Exact"
  * Added synonym "retinoic acid degradation" to GO:0034653
  * Changed synonym scope of GO:0034653 from "Related" to "Exact"
  * Added synonym "vitamin A1 acid catabolic process" to GO:0034653
  * Changed synonym scope of GO:0034653 from "Related" to "Exact"
  * Copied GO:0034653 to GO:0042363 with type OBO_REL:is_a
  * Copied GO:0034653 to GO:0042573 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034653
* Deleted GO:0000747 --part_of--> GO:0022413
* Deleted GO:0001745 --part_of--> GO:0007455
* Deleted GO:0001841 --part_of--> GO:0001839
* Copied GO:0001842 to GO:0001839 with type part_of
* Deleted GO:0001981 --part_of--> GO:0003018
* Copied GO:0001981 to GO:0003018 with type OBO_REL:is_a
* Copied GO:0002234 to GO:0009595 with type OBO_REL:is_a
* Copied GO:0002235 to GO:0009595 with type OBO_REL:is_a
* Copied GO:0002235 to GO:0009593 with type OBO_REL:is_a
* Copied GO:0002236 to GO:0009595 with type OBO_REL:is_a
* Copied GO:0002236 to GO:0009593 with type OBO_REL:is_a
* Copied GO:0002237 to GO:0042221 with type OBO_REL:is_a
* Copied GO:0002238 to GO:0042221 with type OBO_REL:is_a
* Copied GO:0005513 to GO:0051592 with type OBO_REL:is_a
* Changed definition of GO:0009719 from "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an endogenous stimulus." to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism."
* Copied GO:0009720 to GO:0009593 with type OBO_REL:is_a
* Deleted GO:0009726 --part_of--> GO:0009719
* Copied GO:0009726 to GO:0009719 with type OBO_REL:is_a
* Deleted GO:0009730 --OBO_REL:is_a--> GO:0009726
* Copied GO:0009752 to GO:0009593 with type OBO_REL:is_a
* Copied GO:0009754 to GO:0009593 with type OBO_REL:is_a
* Copied GO:0009754 to GO:0009726 with type OBO_REL:is_a
* Deleted GO:0014022 --OBO_REL:is_a--> GO:0009653
* Deleted GO:0014022 --part_of--> GO:0001840
* Copied GO:0014022 to GO:0002011 with type OBO_REL:is_a
* Copied GO:0014022 to GO:0001839 with type part_of
* Copied GO:0016047 to GO:0009603 with type OBO_REL:is_a
* Copied GO:0016052 to GO:0009056 with type OBO_REL:is_a
* Added synonym "iron-sulfur cluster biosynthesis" to GO:0016226
* Changed synonym scope of GO:0016226 from "Related" to "Exact"
* Deleted GO:0021990 --part_of--> GO:0001840
* Copied GO:0021990 to GO:0001839 with type part_of
* Deleted GO:0021991 --part_of--> GO:0001840
* Copied GO:0021991 to GO:0001839 with type part_of
* Changed definition of GO:0030075 from "A membraneous cellular structure derived from, but not necessarily continuous with, the plasma membrane. It bears the photosynthetic pigments in photosynthetic bacteria." to "A thylakoid that is derived from and attached to, but not necessarily continuous with, the plasma membrane, and is not enclosed in a plastid. It bears the photosynthetic pigments in photosynthetic cyanobacteria."
* Deleted synonym "thylakoid (sensu Bacteria)" from GO:0030075
* Deleted GO:0030094 --OBO_REL:is_a--> GO:0044433
* Deleted GO:0030094 --OBO_REL:is_a--> GO:0044435
* Deleted GO:0030096 --OBO_REL:is_a--> GO:0044435
* Deleted GO:0030096 --OBO_REL:is_a--> GO:0044433
* Added synonym "metallo-sulfur cluster biosynthesis" to GO:0031163
* Changed synonym scope of GO:0031163 from "Related" to "Exact"
* Added synonym "metallo-sulphur cluster assembly" to GO:0031163
* Changed synonym scope of GO:0031163 from "Related" to "Exact"
* Deleted GO:0031163 --OBO_REL:is_a--> GO:0051186
* Copied GO:0031163 to GO:0051188 with type OBO_REL:is_a
* Copied GO:0031318 to GO:0009594 with type OBO_REL:is_a
* Deleted GO:0031676 --OBO_REL:is_a--> GO:0044433
* Changed definition of GO:0033105 from "The membrane-like structure, composed of glycolipids and proteins, that encloses the pigments and other contents of the chlorosome." to "The structure, composed of a monolayer of glycolipids with embedded proteins, that encloses the pigments and other contents of the chlorosome."
* Added definition dbxref PMID:17303128 to GO:0033105
* Deleted GO:0033105 --OBO_REL:is_a--> GO:0044446
* Copied GO:0033105 to GO:0034646 with type OBO_REL:is_a
* Deleted GO:0034430 --OBO_REL:is_a--> GO:0044446
* Copied GO:0034430 to GO:0034646 with type OBO_REL:is_a
* Deleted GO:0042716 --OBO_REL:is_a--> GO:0016023
* Copied GO:0042716 to GO:0044444 with type OBO_REL:is_a
* Copied GO:0042769 to GO:0051606 with type OBO_REL:is_a
* Deleted GO:0048493 --OBO_REL:is_a--> GO:0044433

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