[Go-diff] GO update 01/13/2009

Tue Jan 13 21:30:48 PST 2009

OBODIFF of gene_ontology_write.obo version 1.380 by 1.386

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010859
* Created object of type obo:TERM with id GO:0010860
* Created object of type obo:TERM with id GO:0010861
* Created object of type obo:TERM with id GO:0070250
* Created object of type obo:TERM with id GO:0070251
* Populated new object GO:0010859 (macro)
  * Changed name of GO:0010859 from "<new term>" to "calcium-dependent cysteine-type endopeptidase inhibitor activity"
  * Set definition of GO:0010859 to "Stops, prevents or reduces the activity of a calcium-dependent cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile in a calcium-dependent manner."
  * Added definition dbxref GOC:dph to GO:0010859
  * Added definition dbxref GOC:tb to GO:0010859
  * Copied GO:0010859 to GO:0004869 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0010859
* Populated new object GO:0010860 (macro)
  * Changed name of GO:0010860 from "<new term>" to "proteasome regulator activity"
  * Set definition of GO:0010860 to "Modulates the activity of the proteasome complex. The proteasome complex performs regulated ubiquitin-dependent cytosolic and nuclear proteolysis."
  * Added definition dbxref GOC:dph to GO:0010860
  * Added definition dbxref GOC:tb to GO:0010860
  * Copied GO:0010860 to GO:0003674 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0010860
* Populated new object GO:0010861 (macro)
  * Changed name of GO:0010861 from "<new term>" to "thyroid hormone receptor activator activity"
  * Set definition of GO:0010861 to "Any transcription regulator activity required for initiation or upregulation of transcription."
  * Added definition dbxref GOC:dph to GO:0010861
  * Added definition dbxref GOC:tb to GO:0010861
  * Copied GO:0010861 to GO:0030546 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0010861
* Populated new object GO:0070250 (macro)
  * Changed name of GO:0070250 from "<new term>" to "mating projection membrane"
  * Set definition of GO:0070250 to "The portion of the plasma membrane surrounding a mating projection, the projection formed by unicellular fungi in response to mating pheromone."
  * Added definition dbxref GOC:jp to GO:0070250
  * Added synonym "shmoo membrane" to GO:0070250
  * Added general dbxref GOC:jp to synonym shmoo membrane of GO:0070250
  * Changed synonym scope of GO:0070250 from "Related" to "Narrow"
  * Copied GO:0070250 to GO:0005937 with type part_of
  * Copied GO:0070250 to GO:0031253 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070250
* Populated new object GO:0070251 (macro)
  * Changed name of GO:0070251 from "<new term>" to "pristanate-CoA ligase activity"
  * Set definition of GO:0070251 to "Catalysis of the reaction: ATP + pristanate + CoA = AMP + diphosphate + pristanoyl-CoA."
  * Added definition dbxref GOC:pde to GO:0070251
  * Added definition dbxref PMID:10198260 to GO:0070251
  * Added general dbxref EC:6.2.1.24 to GO:0070251
  * Added general dbxref MetaCyc:PHYTANATE--COA-LIGASE-RXN to GO:0070251
  * Added GO:0070251 to category gosubset_prok
  * Added synonym "pristanate:CoA ligase (AMP-forming)" to GO:0070251
  * Added general dbxref GOc:mah to synonym pristanate:CoA ligase (AMP-forming) of GO:0070251
  * Changed synonym scope of GO:0070251 from "Related" to "Exact"
  * Added synonym "pristanoyl-CoA ligase activity" to GO:0070251
  * Added general dbxref GOC:mah to synonym pristanoyl-CoA ligase activity of GO:0070251
  * Changed synonym scope of GO:0070251 from "Related" to "Exact"
  * Copied GO:0070251 to GO:0016878 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070251
* Deleted synonym "<new synonym>negative regulation of cytokine mediated signaling pathway" from GO:0001960
* Added synonym "negative regulation of cytokine mediated signaling pathway" to GO:0001960
* Added general dbxref GOC:tb to synonym negative regulation of cytokine mediated signaling pathway of GO:0001960
* Added general dbxref GOC:dph to synonym negative regulation of cytokine mediated signaling pathway of GO:0001960
* Changed synonym scope of GO:0001960 from "Related" to "Exact"
* Deleted GO:0002032 --OBO_REL:is_a--> GO:0043393
* Copied GO:0002032 to GO:0032091 with type OBO_REL:is_a
* Changed name of GO:0002045 from "regulation of cell adhesion during intussusceptive angiogenesis" to "regulation of cell adhesion involved in intussusceptive angiogenesis"
* Changed definition of GO:0002045 from "The process that modulates the frequency, rate or extent of attachment of a blood vessel endothelial cell to another cell or to the extracellular matrix during intussusceptive angiogenesis." to "The process that modulates the frequency, rate or extent of attachment of a blood vessel endothelial cell to another cell or to the extracellular matrix involved in intussusceptive angiogenesis."
* Changed synonym scope of GO:0003918 from "Narrow" to "Exact"
* Changed name of GO:0004869 from "cysteine-type peptidase inhibitor activity" to "cysteine-type endopeptidase inhibitor activity"
* Changed definition of GO:0004869 from "Stops, prevents or reduces the activity of a cysteine-type peptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile." to "Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile."
* Changed definition of GO:0005782 from "MERGED DEFINITION:
TARGET DEFINITION: The material contained within the membrane of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
--------------------
SOURCE DEFINITION: The volume enclosed by the membranes of a peroxisome." to "The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase."
* Deleted definition dbxref GOC:mah from GO:0005782
* Added definition dbxref GOC:curators to GO:0005782
* Changed name of GO:0007257 from "activation of JNK activity" to "activation of JUN kinase activity"
* Deleted GO:0008538 --OBO_REL:is_a--> GO:0008047
* Copied GO:0008538 to GO:0010860 with type OBO_REL:is_a
* Deleted GO:0008539 --OBO_REL:is_a--> GO:0004857
* Copied GO:0008539 to GO:0010860 with type OBO_REL:is_a
* Changed name of GO:0008657 from "DNA gyrase inhibitor activity" to "DNA topoisomerase (ATP-hydrolyzing) inhibitor activity"
* Changed definition of GO:0008657 from "Stops, prevents or reduces the activity of DNA gyrase." to "Stops, prevents or reduces the activity of ATP-hydrolyzing DNA topoisomerase. ATP-hydrolyzing DNA topoisomerase catalyzes the DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2."
* Added synonym "DNA gyrase inhibitor activity" to GO:0008657
* Added general dbxref GOC:tb to synonym DNA gyrase inhibitor activity of GO:0008657
* Added general dbxref GOC:dph to synonym DNA gyrase inhibitor activity of GO:0008657
* Changed synonym scope of GO:0008657 from "Related" to "Exact"
* Deleted GO:0016534 --OBO_REL:is_a--> GO:0030295
* Copied GO:0016534 to GO:0043539 with type OBO_REL:is_a
* Set definition of GO:0017114 to "Stops, prevents or reduces the activity of a protease by a wide-spectrum protease inhibitor. A wide-spectrum protease inhibitor is a protein having a peptide stretch which contains specific cleavage sites for different proteinases enabling inhibition of all four classes of proteinases by formation of a covalent bond between the inhibitor and the protease."
* Added definition dbxref GOC:dph to GO:0017114
* Added definition dbxref GOC:tb to GO:0017114
* Deleted GO:0017114 --OBO_REL:is_a--> GO:0004866
* Copied GO:0017114 to GO:0030414 with type OBO_REL:is_a
* Changed name of GO:0017163 from "negative regulator of basal transcription activity" to "basal transcription repressor activity"
* Set definition of GO:0017163 to "Any transcription regulator activity that prevents or downregulates basal transcription.  Basal transcription results from transcription that is controlled by the minimal complement of proteins necessary to reconstitute transcription from a minimal promoter."
* Added definition dbxref GOC:dph to GO:0017163
* Added definition dbxref GOC:tb to GO:0017163
* Added definition dbxref http://tfib.med.harvard.edu/transcription/basaltx.html to GO:0017163
* Deleted GO:0017163 --OBO_REL:is_a--> GO:0030528
* Copied GO:0017163 to GO:0016564 with type OBO_REL:is_a
* Deleted GO:0030161 --OBO_REL:is_a--> GO:0004869
* Copied GO:0030161 to GO:0010859 with type OBO_REL:is_a
* Set definition of GO:0030374 to "The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself."
* Added definition dbxref GOC:dph to GO:0030374
* Added definition dbxref GOC:tb to GO:0030374
* Set definition of GO:0030375 to "The function of a transcription cofactor that activates transcription in conjuction with a thyroid hormone-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself."
* Added definition dbxref GOC:dph to GO:0030375
* Added definition dbxref GOC:tb to GO:0030375
* Copied GO:0030375 to GO:0010861 with type OBO_REL:is_a
* Changed name of GO:0030567 from "prothrombin activator activity" to "thrombin activator activity"
* Added synonym "prothrombin activator activity" to GO:0030567
* Added general dbxref GOC:tb to synonym prothrombin activator activity of GO:0030567
* Added general dbxref GOC:dph to synonym prothrombin activator activity of GO:0030567
* Changed name of GO:0032234 from "regulation of calcium ion transport via store-operated calcium channel" to "regulation of calcium ion transport via store-operated calcium channel activity"
* Changed name of GO:0032235 from "negative regulation of calcium ion transport via store-operated calcium channel" to "negative regulation of calcium ion transport via store-operated calcium channel activity"
* Changed name of GO:0032236 from "positive regulation of calcium ion transport via store-operated calcium channel" to "positive regulation of calcium ion transport via store-operated calcium channel activity"
* Deleted GO:0040030 --OBO_REL:is_a--> GO:0040029
* Deleted GO:0043027 --OBO_REL:is_a--> GO:0004866
* Copied GO:0043027 to GO:0004869 with type OBO_REL:is_a
* Changed name of GO:0043506 from "regulation of JNK activity" to "regulation of JUN kinase activity"
* Changed name of GO:0043507 from "positive regulation of JNK activity" to "positive regulation of JUN kinase activity"
* Changed name of GO:0043508 from "negative regulation of JNK activity" to "negative regulation of JUN kinase activity"
* Deleted GO:0045857 --OBO_REL:is_a--> GO:0045814
* Deleted GO:0045858 --OBO_REL:is_a--> GO:0045815
* Changed name of GO:0051925 from "regulation of calcium ion transport via voltage-gated calcium channel" to "regulation of calcium ion transport via voltage-gated calcium channel activity"
* Changed name of GO:0051927 from "negative regulation of calcium ion transport via voltage-gated calcium channel" to "negative regulation of calcium ion transport via voltage-gated calcium channel activity"
* Changed name of GO:0051929 from "positive regulation of calcium ion transport via voltage-gated calcium channel" to "positive regulation of calcium ion transport via voltage-gated calcium channel activity"
* Deleted GO:0070242 --part_of--> GO:0043029