[Go-diff] GO update 04/02/2009

Thu Apr 2 21:30:52 PDT 2009

OBODIFF of gene_ontology_write.obo version 1.508 by 1.511

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0060466
* Created object of type obo:TERM with id GO:0060467
* Created object of type obo:TERM with id GO:0060468
* Created object of type obo:TERM with id GO:0060469
* Created object of type obo:TERM with id GO:0060470
* Created object of type obo:TERM with id GO:0060471
* Created object of type obo:TERM with id GO:0060472
* Created object of type obo:TERM with id GO:0060473
* Created object of type obo:TERM with id GO:0060474
* Created object of type obo:TERM with id GO:0060475
* Created object of type obo:TERM with id GO:0060476
* Created object of type obo:TERM with id GO:0060477
* Created object of type obo:TERM with id GO:0060478
* Created object of type obo:TERM with id GO:0070549
* Created object of type obo:TERM with id GO:0070550
* Populated new object GO:0060466 (macro)
  * Changed name of GO:0060466 from "<new term>" to "activation of meiosis involved in egg activation"
  * Set definition of GO:0060466 to "Any process that starts the inactive process of meiosis in an egg after the egg has been fertilized or physiologically activated. Eggs generally arrest in meiosis and complete the process after activation."
  * Added definition dbxref GOC:dph to GO:0060466
  * Added synonym "reactivation of meiosis after fertilization" to GO:0060466
  * Added general dbxref GOC:dph to synonym reactivation of meiosis after fertilization of GO:0060466
  * Changed synonym scope of GO:0060466 from "Related" to "Narrow"
  * Added synonym "resumption of meiosis involved in egg activation" to GO:0060466
  * Added general dbxref GOC:dph to synonym resumption of meiosis involved in egg activation of GO:0060466
  * Changed synonym scope of GO:0060466 from "Related" to "Exact"
  * Copied GO:0060466 to GO:0045836 with type OBO_REL:is_a
  * Copied GO:0060466 to GO:0007343 with type part_of
  * Assigned namespace "biological_process" to GO:0060466
* Populated new object GO:0060467 (macro)
  * Changed name of GO:0060467 from "<new term>" to "negative regulation of fertilization"
  * Set definition of GO:0060467 to "Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)."
  * Added definition dbxref GOC:dph to GO:0060467
  * Copied GO:0060467 to GO:0009566 with type negatively_regulates
  * Copied GO:0060467 to GO:0048519 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060467
* Populated new object GO:0060468 (macro)
  * Changed name of GO:0060468 from "<new term>" to "prevention of polyspermy"
  * Set definition of GO:0060468 to "The negative regulation of fertilization process that takes place as part of egg activation, ensuring that only a single sperm fertilizes the egg."
  * Added definition dbxref GOC:dph to GO:0060468
  * Added synonym "negative regulation of fertilization involved in egg activation" to GO:0060468
  * Added general dbxref GOC:dph to synonym negative regulation of fertilization involved in egg activation of GO:0060468
  * Changed synonym scope of GO:0060468 from "Related" to "Exact"
  * Added synonym "polyspermy block" to GO:0060468
  * Added general dbxref GOC:dph to synonym polyspermy block of GO:0060468
  * Changed synonym scope of GO:0060468 from "Related" to "Exact"
  * Copied GO:0060468 to GO:0007343 with type part_of
  * Copied GO:0060468 to GO:0060467 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060468
* Populated new object GO:0060469 (macro)
  * Changed name of GO:0060469 from "<new term>" to "positive regulation of transcription involved in egg activation"
  * Set definition of GO:0060469 to "Any process that increases the rate, frequency or extent of transcription as a part of the process of egg activation."
  * Added definition dbxref GOC:dph to GO:0060469
  * Added synonym "activation of the egg genome" to GO:0060469
  * Added general dbxref GOC:dph to synonym activation of the egg genome of GO:0060469
  * Added synonym "activation of the maternal genome" to GO:0060469
  * Added general dbxref GOC:dph to synonym activation of the maternal genome of GO:0060469
  * Copied GO:0060469 to GO:0007343 with type part_of
  * Copied GO:0060469 to GO:0045941 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060469
* Populated new object GO:0060470 (macro)
  * Changed name of GO:0060470 from "<new term>" to "elevation of cytosolic calcium ion concentration involved in egg activation"
  * Set definition of GO:0060470 to "The process that increases the concentration of calcium ions in the cytosol after fertilization or the physiological activation of an egg."
  * Added definition dbxref GOC:dph to GO:0060470
  * Copied GO:0060470 to GO:0007204 with type OBO_REL:is_a
  * Copied GO:0060470 to GO:0007343 with type part_of
  * Assigned namespace "biological_process" to GO:0060470
* Populated new object GO:0060471 (macro)
  * Changed name of GO:0060471 from "<new term>" to "cortical granule exocytosis"
  * Set definition of GO:0060471 to "The process of secretion by a cell that results in the release of intracellular molecules contained within a cortical granule by fusion of the vesicle with the plasma membrane of a cell. A cortical granule is a specialized secretory vesicle that is released during egg activation that changes the surface of the egg to prevent polyspermy."
  * Added definition dbxref GOC:dph to GO:0060471
  * Added synonym "cortical granule release" to GO:0060471
  * Added general dbxref GOC:dph to synonym cortical granule release of GO:0060471
  * Copied GO:0060471 to GO:0017156 with type OBO_REL:is_a
  * Copied GO:0060471 to GO:0060468 with type part_of
  * Assigned namespace "biological_process" to GO:0060471
* Populated new object GO:0060472 (macro)
  * Changed name of GO:0060472 from "<new term>" to "positive regulation of cortical granule exocytosis by elevation of cytosolic calcium ion concentration"
  * Set definition of GO:0060472 to "Any process that activates or increases the frequency, rate or extent of cortical granule exocytosis by directing movement of calcium ions (Ca2+) into the cytosol."
  * Added definition dbxref GOC:dph to GO:0060472
  * Copied GO:0060472 to GO:0045956 with type OBO_REL:is_a
  * Copied GO:0060472 to GO:0060471 with type positively_regulates
  * Copied GO:0060472 to GO:0060470 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060472
* Populated new object GO:0060473 (macro)
  * Changed name of GO:0060473 from "<new term>" to "cortical granule"
  * Set definition of GO:0060473 to "A secretory vesicle that is stored under the cell membrane of an egg. These vesicles fuse with the egg plasma membrane as part of egg activation and are part of the block to polyspermy."
  * Added definition dbxref GOC:dph to GO:0060473
  * Added synonym "cortical vesicle" to GO:0060473
  * Added general dbxref GOC:dph to synonym cortical vesicle of GO:0060473
  * Copied GO:0060473 to GO:0030141 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0060473
* Populated new object GO:0060474 (macro)
  * Changed name of GO:0060474 from "<new term>" to "positive regulation of sperm motility involved in capacitation"
  * Set definition of GO:0060474 to "The process by which the controlled movement of a sperm cell is initiated as part of the process required for sperm to reach fertilization competence."
  * Added definition dbxref GOC:dph to GO:0060474
  * Copied GO:0060474 to GO:0048240 with type part_of
  * Copied GO:0060474 to GO:0040017 with type OBO_REL:is_a
  * Copied GO:0060474 to GO:0030317 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0060474
* Populated new object GO:0060475 (macro)
  * Changed name of GO:0060475 from "<new term>" to "positive regulation of actin filament polymerization involved in acrosome reaction"
  * Set definition of GO:0060475 to "Any process that activates or increases the frequency, rate or extent of actin polymerization as part of the acrosome reaction."
  * Added definition dbxref GOC:dph to GO:0060475
  * Added synonym "positive regulation of actin polymerization involved in acrosome reaction" to GO:0060475
  * Added general dbxref GOC:dph to synonym positive regulation of actin polymerization involved in acrosome reaction of GO:0060475
  * Copied GO:0060475 to GO:0007340 with type part_of
  * Copied GO:0060475 to GO:0030838 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060475
* Populated new object GO:0060476 (macro)
  * Changed name of GO:0060476 from "<new term>" to "protein localization involved in acrosome reaction"
  * Set definition of GO:0060476 to "The actin-based process by which a protein is transported to, or maintained in, a specific location in the sperm as part of the acrosome reaction."
  * Added definition dbxref GOC:dph to GO:0060476
  * Copied GO:0060476 to GO:0007340 with type part_of
  * Copied GO:0060476 to GO:0030029 with type OBO_REL:is_a
  * Copied GO:0060476 to GO:0034613 with type OBO_REL:is_a
  * Copied GO:0060476 to GO:0008105 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060476
* Populated new object GO:0060477 (macro)
  * Changed name of GO:0060477 from "<new term>" to "peptidyl-serine phosphorylation involved in acrosome reaction"
  * Set definition of GO:0060477 to "The posttranslational phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine that is part of the acrosome reaction."
  * Added definition dbxref GOC:dph to GO:0060477
  * Copied GO:0060477 to GO:0018105 with type OBO_REL:is_a
  * Copied GO:0060477 to GO:0007340 with type part_of
  * Assigned namespace "biological_process" to GO:0060477
* Populated new object GO:0060478 (macro)
  * Changed name of GO:0060478 from "<new term>" to "acrosomal vesicle exocytosis"
  * Set definition of GO:0060478 to "The release of intracellular molecules contained within the acrosomal granule by fusion of the vesicle with the plasma membrane of the oocyte, requiring calcium ions."
  * Added definition dbxref GOC:dph to GO:0060478
  * Added synonym "acrosomal granule exocytosis" to GO:0060478
  * Added general dbxref GOC:dph to synonym acrosomal granule exocytosis of GO:0060478
  * Added synonym "acrosome exocytosis" to GO:0060478
  * Added general dbxref GOC:dph to synonym acrosome exocytosis of GO:0060478
  * Changed synonym scope of GO:0060478 from "Related" to "Exact"
  * Copied GO:0060478 to GO:0007340 with type part_of
  * Copied GO:0060478 to GO:0017156 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060478
* Populated new object GO:0070549 (macro)
  * Changed name of GO:0070549 from "<new term>" to "RNA interference, negative regulation of translation"
  * Set definition of GO:0070549 to "A process of negative regulation of translation that is mediated by the association of small interfering RNAs (siRNAs) with a cognate target mRNA."
  * Added definition dbxref GOC:mah to GO:0070549
  * Added definition dbxref PMID:18771919 to GO:0070549
  * Added synonym "RNA interference, down regulation of translation" to GO:0070549
  * Changed synonym scope of GO:0070549 from "Related" to "Exact"
  * Added synonym "RNA interference, down-regulation of translation" to GO:0070549
  * Changed synonym scope of GO:0070549 from "Related" to "Exact"
  * Added synonym "RNA interference, downregulation of translation" to GO:0070549
  * Changed synonym scope of GO:0070549 from "Related" to "Exact"
  * Added synonym "RNA interference, inhibition of translation" to GO:0070549
  * Changed synonym scope of GO:0070549 from "Related" to "Narrow"
  * Copied GO:0070549 to GO:0016246 with type part_of
  * Copied GO:0070549 to GO:0040033 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070549
* Populated new object GO:0070550 (macro)
  * Changed name of GO:0070550 from "<new term>" to "rDNA condensation"
  * Set definition of GO:0070550 to "The cell cycle process whereby the chromatin structure of the rDNA repeats is compacted. In S. cerevisiae, condensation and resolution of the rDNA occurs during anaphasep"
  * Added definition dbxref GOC:df to GO:0070550
  * Added definition dbxref PMID:10811823 to GO:0070550
  * Added definition dbxref PMID:15137940 to GO:0070550
  * Copied GO:0070550 to GO:0007076 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070550
* Changed name of GO:0001669 from "acrosome" to "acrosomal vesicle"
* Added synonym "acrosome" to GO:0001669
* Added general dbxref GOC:dph to synonym acrosome of GO:0001669
* Changed name of GO:0002078 from "membrane fusion during acrosome reaction" to "membrane fusion involved in acrosome reaction"
* Set definition of GO:0003826 to "Catalysis of an oxidation-reduction (redox) reaction involving an alpha-ketoacid."
* Added definition dbxref GOC:mah to GO:0003826
* Set definition of GO:0004147 to "Catalysis of the reaction: acyl-CoA + dihydrolipoamide = CoA + S-acyldihydrolipoamide, where the acyl group is a branched chain."
* Added definition dbxref GOC:mah to GO:0004147
* Set definition of GO:0004583 to "Catalysis of the transfer of an alpha-D-glucosyl residue from dolichyl-phosphate D-glucose into a membrane lipid-linked oligosaccharide."
* Added definition dbxref GOC:mah to GO:0004583
* Set definition of GO:0004753 to "Catalysis of the cleavage of N6-(L-1,3-dicarboxypropyl)-L-lysine to release an amino acid (lysine or glutamate), with the concomitant reduction of an electron acceptor."
* Added definition dbxref GOC:mah to GO:0004753
* Set definition of GO:0004779 to "Catalysis of the transfer of an adenylyl group from an adenosine nucleotide (ATP or ADP) to sulfate, forming adenylylsulfate."
* Added definition dbxref GOC:mah to GO:0004779
* Added definition dbxref MetaCyc:SULFATE-ADENYLYLTRANS-RXN to GO:0004779
* Added definition dbxref MetaCyc:SULFATE-ADENYLYLTRANSFERASE-(ADP)-RXN to GO:0004779
* Deleted GO:0006446 --OBO_REL:is_a--> GO:0050794
* Changed definition of GO:0007076 from "The cell cycle process whereby chromatin structure is compacted prior to mitosis in eukaryotic cells." to "The cell cycle process whereby chromatin structure is compacted prior to and during mitosis in eukaryotic cells."
* Changed definition of GO:0007340 from "The discharge, by sperm, of a single, anterior secretory granule following their attachment to the zona pellucida surrounding the oocyte. The process begins with the fusion of the outer acrosomal membrane with the sperm plasma membrane and ends with the disperasl of the acrosomal contents into the egg." to "The discharge, by sperm, of a single, anterior secretory granule following the sperm's attachment to the zona pellucida surrounding the oocyte. The process begins with the fusion of the outer acrosomal membrane with the sperm plasma membrane and ends with the exocytosis of the acrosomal contents into the egg."
* Deleted GO:0007340 --OBO_REL:is_a--> GO:0017156
* Copied GO:0007340 to GO:0048610 with type OBO_REL:is_a
* Deleted GO:0010104 --OBO_REL:is_a--> GO:0009966
* Deleted GO:0010105 --OBO_REL:is_a--> GO:0009968
* Deleted GO:0010695 --OBO_REL:is_a--> GO:0032886
* Changed definition of GO:0016246 from "The process by which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and occurs through a specific decrease in the level of mRNA of both host genes and transgenes." to "The process by which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes."
* Added definition dbxref PMID:18771919 to GO:0016246
* Added general dbxref GOC:mah to synonym spinal cord dorsal-ventral patterning of GO:0021513
* Added general dbxref GOC:mah to synonym forebrain dorsal-ventral pattern formation of GO:0021798
* Deleted GO:0045855 --OBO_REL:is_a--> GO:0044087
* Deleted GO:0045856 --OBO_REL:is_a--> GO:0048518
* Deleted GO:0045947 --OBO_REL:is_a--> GO:0048523
* Deleted GO:0045948 --OBO_REL:is_a--> GO:0048522
* Deleted general dbxref GOC:kad from synonym histidine:pyruvate aminotransferase activity of GO:0047312
* Added general dbxref EC:2.6.1.58 to synonym histidine:pyruvate aminotransferase activity of GO:0047312
* Copied GO:0048240 to GO:0048610 with type OBO_REL:is_a
* Deleted GO:0051279 --OBO_REL:is_a--> GO:0032844
* Deleted GO:0051279 --OBO_REL:is_a--> GO:0050794
* Deleted GO:0051280 --OBO_REL:is_a--> GO:0048523
* Deleted GO:0051280 --OBO_REL:is_a--> GO:0032845
* Deleted GO:0051281 --OBO_REL:is_a--> GO:0032846
* Deleted GO:0051281 --OBO_REL:is_a--> GO:0048522
* Copied GO:0060465 to GO:0055123 with type part_of
* Deleted GO:0070514 --OBO_REL:is_a--> GO:0044428