From gocvs at genome.stanford.edu  Mon Jun  2 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Mon, 2 Jun 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 06/02/2008
Message-ID: <200806030430.VAA13847@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.85 by 1.88

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010603
* Created object of type obo:TERM with id GO:0010604
* Created object of type obo:TERM with id GO:0010605
* Created object of type obo:TERM with id GO:0010606
* Created object of type obo:TERM with id GO:0010607
* Created object of type obo:TERM with id GO:0010608
* Created object of type obo:TERM with id GO:0010609
* Created object of type obo:TERM with id GO:0010610
* Created object of type obo:TERM with id GO:0034481
* Created object of type obo:TERM with id GO:0034482
* Created object of type obo:TERM with id GO:0034483
* Created object of type obo:TERM with id GO:0034484
* Created object of type obo:TERM with id GO:0034485
* Created object of type obo:TERM with id GO:0034486
* Created object of type obo:TERM with id GO:0034487
* Created object of type obo:TERM with id GO:0034488
* Created object of type obo:TERM with id GO:0034489
* Created object of type obo:TERM with id GO:0034490
* Created object of type obo:TERM with id GO:0034491
* Created object of type obo:TERM with id GO:0034492
* Created object of type obo:TERM with id GO:0034493
* Created object of type obo:TERM with id GO:0034494
* Created object of type obo:TERM with id GO:0034495
* Populated new object GO:0010603 (macro)
  * Changed name of GO:0010603 from "<new term>" to "regulation of cytoplasmic mRNA processing body assembly"
  * Set definition of GO:0010603 to "Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body."
  * Added definition dbxref GOC:dph to GO:0010603
  * Added definition dbxref GOC:krc to GO:0010603
  * Added definition dbxref GOC:tb to GO:0010603
  * Copied GO:0010603 to GO:0060255 with type OBO_REL:is_a
  * Copied GO:0010603 to GO:0033962 with type regulates
  * Assigned namespace "biological_process" to GO:0010603
* Populated new object GO:0010604 (macro)
  * Changed name of GO:0010604 from "<new term>" to "positive regulation of macromolecule metabolic process"
  * Set definition of GO:0010604 to "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass."
  * Added definition dbxref GOC:dph to GO:0010604
  * Added definition dbxref GOC:tb to GO:0010604
  * Copied GO:0010604 to GO:0060255 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010604
* Populated new object GO:0010605 (macro)
  * Changed name of GO:0010605 from "<new term>" to "negative regulation of macromolecule metabolic process"
  * Set definition of GO:0010605 to "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass."
  * Added definition dbxref GOC:dph to GO:0010605
  * Added definition dbxref GOC:tb to GO:0010605
  * Copied GO:0010605 to GO:0060255 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010605
* Populated new object GO:0010606 (macro)
  * Changed name of GO:0010606 from "<new term>" to "positive regulation of cytoplasmic mRNA processing body assembly"
  * Set definition of GO:0010606 to "Any process that increases the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body."
  * Added definition dbxref GOC:dph to GO:0010606
  * Added definition dbxref GOC:krc to GO:0010606
  * Added definition dbxref GOC:tb to GO:0010606
  * Copied GO:0010606 to GO:0010604 with type OBO_REL:is_a
  * Copied GO:0010606 to GO:0010603 with type OBO_REL:is_a
  * Copied GO:0010606 to GO:0033962 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010606
* Populated new object GO:0010607 (macro)
  * Changed name of GO:0010607 from "<new term>" to "negative regulation of cytoplasmic mRNA processing body assembly"
  * Set definition of GO:0010607 to "Any process that decreases the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body."
  * Added definition dbxref GOC:dph to GO:0010607
  * Added definition dbxref GOC:krc to GO:0010607
  * Added definition dbxref GOC:tb to GO:0010607
  * Copied GO:0010607 to GO:0033962 with type negatively_regulates
  * Copied GO:0010607 to GO:0010605 with type OBO_REL:is_a
  * Copied GO:0010607 to GO:0010603 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010607
* Populated new object GO:0010608 (macro)
  * Changed name of GO:0010608 from "<new term>" to "posttranscriptional regulation of gene expression"
  * Set definition of GO:0010608 to "Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript."
  * Added definition dbxref GOC:dph to GO:0010608
  * Added definition dbxref GOC:tb to GO:0010608
  * Copied GO:0010608 to GO:0010468 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010608
* Populated new object GO:0010609 (macro)
  * Changed name of GO:0010609 from "<new term>" to "posttranscriptional regulation of gene expression by mRNA localization"
  * Set definition of GO:0010609 to "Any process that modulates the frequency, rate or extent of gene expression after the production of a mRNA transcript by its transport into, or maintainance in, a specific location within the cell."
  * Added definition dbxref GOC:dph to GO:0010609
  * Added definition dbxref GOC:tb to GO:0010609
  * Copied GO:0010609 to GO:0010608 with type OBO_REL:is_a
  * Copied GO:0010609 to GO:0008298 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010609
* Populated new object GO:0010610 (macro)
  * Changed name of GO:0010610 from "<new term>" to "regulation of mRNA stability involved in response to stress"
  * Set definition of GO:0010610 to "Any process that modulates the propensity of mRNA molecules to degradation that is part of a change in state or activity of a cell as a result of an exogenous disturbance."
  * Added definition dbxref GOC:dph to GO:0010610
  * Added definition dbxref GOC:tb to GO:0010610
  * Copied GO:0010610 to GO:0006950 with type part_of
  * Copied GO:0010610 to GO:0043488 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010610
* Populated new object GO:0034481 (macro)
  * Changed name of GO:0034481 from "<new term>" to "chondroitin sulfotransferase activity"
  * Set definition of GO:0034481 to "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + chondroitin = adenosine 3',5'-bisphosphate + chondroitin sulfate."
  * Added definition dbxref EC:2.8.2.17 to GO:0034481
  * Added definition dbxref EC:2.8.2.5 to GO:0034481
  * Added definition dbxref GOC:mah to GO:0034481
  * Copied GO:0034481 to GO:0008146 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034481
* Populated new object GO:0034482 (macro)
  * Changed name of GO:0034482 from "<new term>" to "chondroitin 2-O-sulfotransferase activity"
  * Set definition of GO:0034482 to "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + chondroitin = adenosine 3',5'-bisphosphate + chondroitin 2'-O-sulfate. Results in sulfation of glucuronic acid and iduronic acid residues."
  * Added definition dbxref PMID:17227754 to GO:0034482
  * Added general dbxref EC:2.8.2.17 to GO:0034482
  * Added general dbxref MetaCyc:CHONDROITIN-6-SULFOTRANSFERASE-RXN to GO:0034482
  * Added synonym "chondroitin 2-O-sulphotransferase activity" to GO:0034482
  * Changed synonym scope of GO:0034482 from "Related" to "Exact"
  * Added synonym "chondroitin 2-sulfotransferase activity" to GO:0034482
  * Changed synonym scope of GO:0034482 from "Related" to "Exact"
  * Copied GO:0034482 to GO:0034481 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034482
* Populated new object GO:0034483 (macro)
  * Changed name of GO:0034483 from "<new term>" to "heparan sulfate sulfotransferase activity"
  * Set definition of GO:0034483 to "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + heparan sulfate = adenosine 3',5'-bisphosphate + sulfated heparan sulfate."
  * Added definition dbxref GOC:mah to GO:0034483
  * Copied GO:0034483 to GO:0008146 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034483
* Populated new object GO:0034484 (macro)
  * Changed name of GO:0034484 from "<new term>" to "raffinose catabolic process"
  * Set definition of GO:0034484 to "The chemical reactions and pathways resulting in the breakdown of raffinose, the trisaccharide beta-D-fructofuranosyl alpha-D-galactopyranosyl-(1->6)-alpha-D-glucopyranoside."
  * Added definition dbxref ChEBI:16634 to GO:0034484
  * Added definition dbxref GOC:mah to GO:0034484
  * Added synonym "raffinose breakdown" to GO:0034484
  * Changed synonym scope of GO:0034484 from "Related" to "Exact"
  * Added synonym "raffinose catabolism" to GO:0034484
  * Changed synonym scope of GO:0034484 from "Related" to "Exact"
  * Added synonym "raffinose degradation" to GO:0034484
  * Changed synonym scope of GO:0034484 from "Related" to "Exact"
  * Copied GO:0034484 to GO:0009313 with type OBO_REL:is_a
  * Copied GO:0034484 to GO:0033530 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034484
* Populated new object GO:0034485 (macro)
  * Changed name of GO:0034485 from "<new term>" to "phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity"
  * Set definition of GO:0034485 to "Catalysis of the reaction: phosphatidylinositol 3,4,5-trisphosphate +
H2O = phosphatidylinositol 3,4-bisphosphate + phosphate."
  * Added definition dbxref GOC:pf to GO:0034485
  * Copied GO:0034485 to GO:0004437 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034485
* Populated new object GO:0034486 (macro)
  * Changed name of GO:0034486 from "<new term>" to "vacuolar transmembrane transport"
  * Set definition of GO:0034486 to "The process whereby a solute is transported from one side of the vacuolar membrane to the other."
  * Added definition dbxref GOC:mah to GO:0034486
  * Copied GO:0034486 to GO:0007034 with type OBO_REL:is_a
  * Copied GO:0034486 to GO:0055085 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034486
* Populated new object GO:0034487 (macro)
  * Changed name of GO:0034487 from "<new term>" to "vacuolar amino acid transport"
  * Set definition of GO:0034487 to "The process whereby an amino acid is transported from one side of the vacuolar membrane to the other."
  * Added definition dbxref GOC:mah to GO:0034487
  * Added synonym "vacuolar amino acid transmembrane transport" to GO:0034487
  * Changed synonym scope of GO:0034487 from "Related" to "Exact"
  * Copied GO:0034487 to GO:0006865 with type OBO_REL:is_a
  * Copied GO:0034487 to GO:0034486 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034487
* Populated new object GO:0034488 (macro)
  * Changed name of GO:0034488 from "<new term>" to "basic amino acid export from vacuole"
  * Set definition of GO:0034488 to "The directed movement of basic amino acids out of the vacuole."
  * Added definition dbxref GOC:mah to GO:0034488
  * Copied GO:0034488 to GO:0015802 with type OBO_REL:is_a
  * Copied GO:0034488 to GO:0032974 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034488
* Populated new object GO:0034489 (macro)
  * Changed name of GO:0034489 from "<new term>" to "neutral amino acid export from vacuole"
  * Set definition of GO:0034489 to "The directed movement of neutral amino acids out of the vacuole."
  * Added definition dbxref GOC:mah to GO:0034489
  * Copied GO:0034489 to GO:0032974 with type OBO_REL:is_a
  * Copied GO:0034489 to GO:0015804 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034489
* Populated new object GO:0034490 (macro)
  * Changed name of GO:0034490 from "<new term>" to "basic amino acid import into vacuole"
  * Set definition of GO:0034490 to "The directed movement of basic amino acids into the vacuole."
  * Added definition dbxref GOC:mah to GO:0034490
  * Copied GO:0034490 to GO:0032975 with type OBO_REL:is_a
  * Copied GO:0034490 to GO:0015802 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034490
* Populated new object GO:0034491 (macro)
  * Changed name of GO:0034491 from "<new term>" to "neutral amino acid import into vacuole"
  * Set definition of GO:0034491 to "The directed movement of neutral amino acids into the vacuole."
  * Added definition dbxref GOC:mah to GO:0034491
  * Copied GO:0034491 to GO:0015804 with type OBO_REL:is_a
  * Copied GO:0034491 to GO:0032975 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034491
* Populated new object GO:0034492 (macro)
  * Changed name of GO:0034492 from "<new term>" to "hydrogenosome lumen"
  * Set definition of GO:0034492 to "The volume enclosed by the hydrogenosome membrane."
  * Added definition dbxref GOC:rph to GO:0034492
  * Copied GO:0034492 to GO:0042566 with type part_of
  * Copied GO:0034492 to GO:0043233 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034492
* Populated new object GO:0034493 (macro)
  * Changed name of GO:0034493 from "<new term>" to "melanosome lumen"
  * Set definition of GO:0034493 to "The volume enclosed by the melanosome membrane."
  * Added definition dbxref GOC:rph to GO:0034493
  * Copied GO:0034493 to GO:0060205 with type OBO_REL:is_a
  * Copied GO:0034493 to GO:0042470 with type part_of
  * Assigned namespace "cellular_component" to GO:0034493
* Populated new object GO:0034494 (macro)
  * Changed name of GO:0034494 from "<new term>" to "microneme lumen"
  * Set definition of GO:0034494 to "The volume enclosed by the microneme membrane."
  * Added definition dbxref GOC:rph to GO:0034494
  * Copied GO:0034494 to GO:0020009 with type part_of
  * Copied GO:0034494 to GO:0043233 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034494
* Populated new object GO:0034495 (macro)
  * Changed name of GO:0034495 from "<new term>" to "protein storage vacuole lumen"
  * Set definition of GO:0034495 to "The volume enclosed by the protein storage vacuole membrane."
  * Added definition dbxref GOC:rph to GO:0034495
  * Copied GO:0034495 to GO:0000326 with type part_of
  * Copied GO:0034495 to GO:0000330 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034495
* Changed definition of GO:0000171 from "Catalysis of the first cleavage in rRNA transcript processing, also involved in mitochondrial RNA processing." to "Catalysis of the site-specific cleavage of RNA by a catalytic RNA_mediated mechanism; substrates include the A3 site in the ITS1 of pre-rRNA."
* Deleted definition dbxref PMID:10690410 from GO:0000171
* Added definition dbxref PMID:17881380 to GO:0000171
* Deleted synonym "heparin sulfate 2-sulfotransferase activity" from GO:0004394
* Added synonym "heparin 2-sulfotransferase activity" to GO:0004394
* Deleted GO:0004394 --OBO_REL:is_a--> GO:0008146
* Copied GO:0004394 to GO:0034483 with type OBO_REL:is_a
* Added synonym "tRNA 5' leader endonuclease activity" to GO:0004526
* Changed synonym scope of GO:0004526 from "Related" to "Exact"
* Deleted synonym "microtubule-associated protein 2 kinase activity" from GO:0004707
* Deleted synonym "microtubule-associated protein kinase activity" from GO:0004707
* Deleted GO:0005329 --OBO_REL:is_a--> GO:0005275
* Copied GO:0005329 to GO:0008504 with type OBO_REL:is_a
* Deleted GO:0005333 --OBO_REL:is_a--> GO:0005275
* Copied GO:0005333 to GO:0008504 with type OBO_REL:is_a
* Deleted GO:0006417 --OBO_REL:is_a--> GO:0010468
* Copied GO:0006417 to GO:0010608 with type OBO_REL:is_a
* Deleted GO:0006867 --OBO_REL:is_a--> GO:0015802
* Copied GO:0006867 to GO:0015804 with type OBO_REL:is_a
* Deleted GO:0006868 --OBO_REL:is_a--> GO:0015802
* Copied GO:0006868 to GO:0015804 with type OBO_REL:is_a
* Added synonym "heparan sulfate binding" to GO:0008201
* Changed definition of GO:0008298 from "Any process by which RNA is transported to, or maintained in, a specific location within the cell." to "Any process by which mRNA is transported to, or maintained in, a specific location within the cell."
* Deleted GO:0008459 --OBO_REL:is_a--> GO:0008146
* Copied GO:0008459 to GO:0034481 with type OBO_REL:is_a
* Changed name of GO:0008467 from "heparin-glucosamine 3-O-sulfotransferase activity" to "[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity"
* Changed definition of GO:0008467 from "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + heparin-glucosamine = adenosine 3',5'-bisphosphate + heparin-glucosamine 3-O-sulfate." to "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate, with a substrate consensus sequence of Glc(N2S>NAc)?6S GlcA GlcN2S*?6S GlcA>IdoA?2S Glc(N2S/NAc)?6S."
* Deleted synonym "[heparan sulfate]-glucosamine 3-sulfotransferase 1" from GO:0008467
* Changed synonym scope of GO:0008467 from "Exact" to "Related"
* Added synonym "heparin-glucosamine 3-O-sulfotransferase activity" to GO:0008467
* Deleted GO:0008467 --OBO_REL:is_a--> GO:0008146
* Copied GO:0008467 to GO:0034483 with type OBO_REL:is_a
* Changed definition of GO:0008504 from "Catalysis of the transfer of monoamines, organic compounds containing one amino group, from one side of the membrane to the other." to "Catalysis of the transfer of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), from one side of the membrane to the other."
* Deleted definition dbxref GOC:ai from GO:0008504
* Added definition dbxref ChEBI:25375 to GO:0008504
* Added definition dbxref GOC:mah to GO:0008504
* Deleted GO:0010175 --OBO_REL:is_a--> GO:0008504
* Copied GO:0010175 to GO:0005275 with type OBO_REL:is_a
* Copied GO:0010557 to GO:0010604 with type OBO_REL:is_a
* Copied GO:0010558 to GO:0010605 with type OBO_REL:is_a
* Changed name of GO:0010577 from "metalloenzyme activitor activity" to "metalloenzyme activator activity"
* Added synonym "heparin proteoglycan biosynthetic process" to GO:0015012
* Added synonym "heparin proteoglycan biosynthetic process, linkage to polypeptide" to GO:0015013
* Added synonym "heparin proteoglycan biosynthetic process, polysaccharide chain biosynthetic process" to GO:0015014
* Added synonym "heparin proteoglycan biosynthetic process, enzymatic modification" to GO:0015015
* Deleted synonym "heparan sulfate sulfotransferase activity" from GO:0015016
* Added synonym "heparin-glucosamine N-sulfotransferase activity" to GO:0015016
* Changed synonym scope of GO:0015016 from "Related" to "Exact"
* Deleted GO:0015016 --OBO_REL:is_a--> GO:0008146
* Copied GO:0015016 to GO:0034483 with type OBO_REL:is_a
* Added synonym "heparin-alpha-glucosaminide N-acetyltransferase activity" to GO:0015019
* Added synonym "[heparan sulfate]-sulfate lyase activity" to GO:0015021
* Changed definition of GO:0015171 from "Catalysis of the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and can combine in linear arrays to form proteins in living organisms." to "Catalysis of the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group."
* Deleted GO:0015222 --OBO_REL:is_a--> GO:0005275
* Copied GO:0015222 to GO:0008504 with type OBO_REL:is_a
* Changed definition of GO:0015844 from "The directed movement of monoamines, organic compounds containing one amino group, into, out of, within or between cells." to "The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of, within or between cells."
* Deleted definition dbxref GOC:ai from GO:0015844
* Added definition dbxref ChEBI:25375 to GO:0015844
* Added definition dbxref GOC:mah to GO:0015844
* Copied GO:0016441 to GO:0010608 with type OBO_REL:is_a
* Added synonym "heparin 6-O-sulfotransferase activity" to GO:0017095
* Deleted GO:0017095 --OBO_REL:is_a--> GO:0008146
* Copied GO:0017095 to GO:0034483 with type OBO_REL:is_a
* Added synonym "heparin proteoglycan catabolic process" to GO:0030200
* Added synonym "heparin proteoglycan metabolic process" to GO:0030201
* Added synonym "heparan sulfate metabolic process" to GO:0030202
* Added synonym "heparan sulfate biosynthetic process" to GO:0030210
* Added synonym "heparan sulfate catabolic process" to GO:0030211
* Added synonym "heparinase activity" to GO:0030305
* Deleted GO:0031647 --OBO_REL:is_a--> GO:0065008
* Copied GO:0031647 to GO:0010608 with type OBO_REL:is_a
* Deleted GO:0031976 --OBO_REL:is_a--> GO:0043231
* Added synonym "vacuolar amino acid export" to GO:0032974
* Changed synonym scope of GO:0032974 from "Related" to "Exact"
* Copied GO:0032974 to GO:0034487 with type OBO_REL:is_a
* Added synonym "vacuolar amino acid import" to GO:0032975
* Changed synonym scope of GO:0032975 from "Related" to "Exact"
* Copied GO:0032975 to GO:0034487 with type OBO_REL:is_a
* Added synonym "heparin-glucosamine 3-sulfotransferase 2 activity" to GO:0033871
* Deleted GO:0033871 --OBO_REL:is_a--> GO:0008146
* Copied GO:0033871 to GO:0034483 with type OBO_REL:is_a
* Added synonym "heparin-glucosamine 3-sulfotransferase 3 activity" to GO:0033872
* Deleted GO:0033872 --OBO_REL:is_a--> GO:0008146
* Copied GO:0033872 to GO:0034483 with type OBO_REL:is_a
* Changed definition of GO:0042046 from "The chemical reactions and pathways involving the W-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear tungsten ion (W) coordinated by one or two molybdopterin ligands." to "The chemical reactions and pathways involving the W-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofator consists of a mononuclear tungsten ion (W) coordinated by one or two molybdopterin ligands."
* Added synonym "heparin N-acetylglucosaminyltransferase activity" to GO:0042328
* Deleted GO:0042649 --OBO_REL:is_a--> GO:0009579
* Deleted GO:0042649 --OBO_REL:is_a--> GO:0043231
* Deleted GO:0042649 --OBO_REL:is_a--> GO:0044435
* Copied GO:0042649 to GO:0031976 with type OBO_REL:is_a
* Deleted GO:0042766 --OBO_REL:is_a--> GO:0006333
* Copied GO:0042766 to GO:0006338 with type OBO_REL:is_a
* Added synonym "heparin proteoglycan binding" to GO:0043395
* Deleted GO:0043487 --OBO_REL:is_a--> GO:0065008
* Copied GO:0043487 to GO:0010608 with type OBO_REL:is_a
* Copied GO:0044425 to GO:0044464 with type OBO_REL:is_a
* Added synonym "heparan sulfate lyase activity" to GO:0047488
* Deleted synonym "chondroitin sulfotransferase activity" from GO:0047756
* Deleted GO:0047756 --OBO_REL:is_a--> GO:0008146
* Copied GO:0047756 to GO:0034481 with type OBO_REL:is_a
* Deleted GO:0051247 --OBO_REL:is_a--> GO:0009893
* Copied GO:0051247 to GO:0010604 with type OBO_REL:is_a
* Deleted GO:0051248 --OBO_REL:is_a--> GO:0009892
* Copied GO:0051248 to GO:0010605 with type OBO_REL:is_a
* Deleted GO:0051937 --OBO_REL:is_a--> GO:0015837
* Copied GO:0051937 to GO:0015844 with type OBO_REL:is_a
* Changed name of GO:0055008 from "cardiac muscle morphogensis" to "cardiac muscle morphogenesis"
* Copied GO:0055008 to GO:0003007 with type part_of

From gocvs at genome.stanford.edu  Tue Jun  3 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Tue, 3 Jun 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 06/03/2008
Message-ID: <200806040430.VAA25617@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.88 by 1.92

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034496
* Created object of type obo:TERM with id GO:0034497
* Created object of type obo:TERM with id GO:0034498
* Created object of type obo:TERM with id GO:0034499
* Created object of type obo:TERM with id GO:0034500
* Created object of type obo:TERM with id GO:0034501
* Created object of type obo:TERM with id GO:0034502
* Created object of type obo:TERM with id GO:0034503
* Created object of type obo:TERM with id GO:0043914
* Created object of type obo:TERM with id GO:0043915
* Created object of type obo:TERM with id GO:0043916
* Created object of type obo:TERM with id GO:0060256
* Created object of type obo:TERM with id GO:0060257
* Created object of type obo:TERM with id GO:0060258
* Created object of type obo:TERM with id GO:0060259
* Created object of type obo:TERM with id GO:0060260
* Created object of type obo:TERM with id GO:0060261
* Populated new object GO:0034496 (macro)
  * Changed name of GO:0034496 from "<new term>" to "multivesicular body membrane disassembly"
  * Set definition of GO:0034496 to "The controlled breakdown of the membranes of multivesicular bodies."
  * Added definition dbxref GOC:rb to GO:0034496
  * Added synonym "MVB membrane disassembly" to GO:0034496
  * Changed synonym scope of GO:0034496 from "Related" to "Exact"
  * Copied GO:0034496 to GO:0030397 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034496
* Populated new object GO:0034497 (macro)
  * Changed name of GO:0034497 from "<new term>" to "protein localization to pre-autophagosomal structure"
  * Set definition of GO:0034497 to "Any process by which a protein is transported to, or maintained at, the pre-autophagosomal structure (PAS)."
  * Added definition dbxref GOC:rb to GO:0034497
  * Added synonym "protein localization to PAS" to GO:0034497
  * Changed synonym scope of GO:0034497 from "Related" to "Exact"
  * Copied GO:0034497 to GO:0008104 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034497
* Populated new object GO:0034498 (macro)
  * Changed name of GO:0034498 from "<new term>" to "early endosome to Golgi transport"
  * Set definition of GO:0034498 to "The directed movement of substances from early endosomes to the Golgi."
  * Added definition dbxref GOC:rb to GO:0034498
  * Added synonym "PGE to Golgi transport" to GO:0034498
  * Changed synonym scope of GO:0034498 from "Related" to "Exact"
  * Added synonym "post-Golgi endosome to Golgi transport" to GO:0034498
  * Changed synonym scope of GO:0034498 from "Related" to "Exact"
  * Copied GO:0034498 to GO:0048193 with type OBO_REL:is_a
  * Copied GO:0034498 to GO:0016197 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034498
* Populated new object GO:0034499 (macro)
  * Changed name of GO:0034499 from "<new term>" to "late endosome to Golgi transport"
  * Set definition of GO:0034499 to "The directed movement of substances from late endosomes to the Golgi."
  * Added definition dbxref GOC:rb to GO:0034499
  * Added synonym "prevacuolar endosome to Golgi transport" to GO:0034499
  * Changed synonym scope of GO:0034499 from "Related" to "Exact"
  * Added synonym "PVE to Golgi transport" to GO:0034499
  * Changed synonym scope of GO:0034499 from "Related" to "Exact"
  * Copied GO:0034499 to GO:0048193 with type OBO_REL:is_a
  * Copied GO:0034499 to GO:0016197 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034499
* Populated new object GO:0034500 (macro)
  * Changed name of GO:0034500 from "<new term>" to "rDNA separation"
  * Set definition of GO:0034500 to "The cell cycle process whereby rDNA repeat regions are physically detached from each other during chromosome separation."
  * Added definition dbxref GOC:mah to GO:0034500
  * Copied GO:0034500 to GO:0051304 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034500
* Populated new object GO:0034501 (macro)
  * Changed name of GO:0034501 from "<new term>" to "protein localization to kinetochore"
  * Set definition of GO:0034501 to "Any process by which a protein is transported to, or maintained at, the kinetochore."
  * Added definition dbxref GOC:mah to GO:0034501
  * Added synonym "condensin localization to kinetochore" to GO:0034501
  * Changed synonym scope of GO:0034501 from "Related" to "Narrow"
  * Copied GO:0034501 to GO:0008104 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034501
* Populated new object GO:0034502 (macro)
  * Changed name of GO:0034502 from "<new term>" to "protein localization to chromosome"
  * Set definition of GO:0034502 to "Any process by which a protein is transported to, or maintained at, a specific location on a chromosome."
  * Added definition dbxref GOC:mah to GO:0034502
  * Added synonym "condensin localization to chromosome" to GO:0034502
  * Changed synonym scope of GO:0034502 from "Related" to "Narrow"
  * Copied GO:0034502 to GO:0008104 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034502
* Populated new object GO:0034503 (macro)
  * Changed name of GO:0034503 from "<new term>" to "protein localization to nucleolar rDNA repeats"
  * Set definition of GO:0034503 to "Any process by which a protein is transported to, or maintained at, the rDNA repeats on a chromosome in the nucleolus."
  * Added definition dbxref GOC:mah to GO:0034503
  * Added synonym "condensin localization to nucleolar rDNA repeats" to GO:0034503
  * Changed synonym scope of GO:0034503 from "Related" to "Narrow"
  * Copied GO:0034503 to GO:0034502 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034503
* Populated new object GO:0043914 (macro)
  * Changed name of GO:0043914 from "<new term>" to "NADPH:sulfur oxidoreductase activity"
  * Set definition of GO:0043914 to "Catalysis of the reaction: NADPH + S0 = H2S + NADP."
  * Added definition dbxref GOC:jl to GO:0043914
  * Added definition dbxref PMID:17449625 to GO:0043914
  * Added general dbxref EC:1.-.-.- to GO:0043914
  * Added general dbxref IMG:03008 to GO:0043914
  * Added GO:0043914 to category gosubset_prok
  * Added synonym "CoA-dependent NAD(P)H sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "coenzyme A-dependent NAD(P)H sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NAD(P)H elemental sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NAD(P)H sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NAD(P)H sulphur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NAD(P)H:sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NADPH:sulphur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NSR" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Copied GO:0043914 to GO:0016491 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043914
* Populated new object GO:0043915 (macro)
  * Changed name of GO:0043915 from "<new term>" to "L-seryl-tRNA(Sec) kinase activity"
  * Set definition of GO:0043915 to "Catalysis of the reaction: ATP + L-seryl-tRNA(Sec) = ADP + O-phospho-L-seryl-tRNA(Sec)."
  * Added definition dbxref GOC:jl to GO:0043915
  * Added definition dbxref IMG:03019 to GO:0043915
  * Added definition dbxref UniProt:Q8IV42 to GO:0043915
  * Added general dbxref EC:2.7.1.- to GO:0043915
  * Added general dbxref IMG:03019 to GO:0043915
  * Added GO:0043915 to category gosubset_prok
  * Added synonym "O-phosphoseryl-tRNA(Sec) kinase activity" to GO:0043915
  * Changed synonym scope of GO:0043915 from "Related" to "Exact"
  * Copied GO:0043915 to GO:0016773 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043915
* Populated new object GO:0043916 (macro)
  * Changed name of GO:0043916 from "<new term>" to "DNA-7-methylguanine glycosylase activity"
  * Set definition of GO:0043916 to "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes the alkylated base 7-methylguanine."
  * Added definition dbxref GOC:jl to GO:0043916
  * Added definition dbxref PMID:16468998 to GO:0043916
  * Added general dbxref EC:3.2.2.- to GO:0043916
  * Added general dbxref IMG:03021 to GO:0043916
  * Added GO:0043916 to category gosubset_prok
  * Copied GO:0043916 to GO:0003905 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043916
* Populated new object GO:0060256 (macro)
  * Changed name of GO:0060256 from "<new term>" to "regulation of flocculation"
  * Set definition of GO:0060256 to "Any process that modulates the rate, frequency or extent of the non-sexual aggregation of single-celled organisms."
  * Added definition dbxref GOC:dph to GO:0060256
  * Added definition dbxref GOC:tb to GO:0060256
  * Copied GO:0060256 to GO:0043900 with type OBO_REL:is_a
  * Copied GO:0060256 to GO:0000128 with type regulates
  * Assigned namespace "biological_process" to GO:0060256
* Populated new object GO:0060257 (macro)
  * Changed name of GO:0060257 from "<new term>" to "negative regulation of flocculation"
  * Set definition of GO:0060257 to "Any process that decreases the rate, frequency or extent of the non-sexual aggregation of single-celled organisms."
  * Added definition dbxref GOC:dph to GO:0060257
  * Added definition dbxref GOC:tb to GO:0060257
  * Copied GO:0060257 to GO:0043901 with type OBO_REL:is_a
  * Copied GO:0060257 to GO:0060256 with type OBO_REL:is_a
  * Copied GO:0060257 to GO:0000128 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0060257
* Populated new object GO:0060258 (macro)
  * Changed name of GO:0060258 from "<new term>" to "negative regulation of filamentous growth"
  * Set definition of GO:0060258 to "Any process that decreases the frequency, rate or extent of the process by which a multicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape."
  * Added definition dbxref GOC:dph to GO:0060258
  * Added definition dbxref GOC:tb to GO:0060258
  * Copied GO:0060258 to GO:0030447 with type negatively_regulates
  * Copied GO:0060258 to GO:0010570 with type OBO_REL:is_a
  * Copied GO:0060258 to GO:0045926 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060258
* Populated new object GO:0060259 (macro)
  * Changed name of GO:0060259 from "<new term>" to "regulation of feeding behavior"
  * Set definition of GO:0060259 to "Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food."
  * Added definition dbxref GOC:dph to GO:0060259
  * Added definition dbxref GOC:tb to GO:0060259
  * Added synonym "regulation of feeding behaviour" to GO:0060259
  * Added general dbxref GOC:tb to synonym regulation of feeding behaviour of GO:0060259
  * Added general dbxref GOC:dph to synonym regulation of feeding behaviour of GO:0060259
  * Changed synonym scope of GO:0060259 from "Related" to "Exact"
  * Copied GO:0060259 to GO:0050795 with type OBO_REL:is_a
  * Copied GO:0060259 to GO:0007631 with type regulates
  * Assigned namespace "biological_process" to GO:0060259
* Populated new object GO:0060260 (macro)
  * Changed name of GO:0060260 from "<new term>" to "regulation of transcription initiation from RNA polymerase II promoter"
  * Set definition of GO:0060260 to "Any process that modulates the rate, frequency or extent of a process involved in starting transcription from the RNA polymerase II promoter."
  * Added definition dbxref GOC:dph to GO:0060260
  * Added definition dbxref GOC:tb to GO:0060260
  * Copied GO:0060260 to GO:0060255 with type OBO_REL:is_a
  * Copied GO:0060260 to GO:0006367 with type regulates
  * Assigned namespace "biological_process" to GO:0060260
* Populated new object GO:0060261 (macro)
  * Changed name of GO:0060261 from "<new term>" to "positive regulation of transcription initiation from RNA polymerase II promoter"
  * Set definition of GO:0060261 to "Any process that increases the rate, frequency or extent of a process involved in starting transcription from the RNA polymerase II promoter."
  * Added definition dbxref GOC:dph to GO:0060261
  * Added definition dbxref GOC:tb to GO:0060261
  * Copied GO:0060261 to GO:0060260 with type OBO_REL:is_a
  * Copied GO:0060261 to GO:0010604 with type OBO_REL:is_a
  * Copied GO:0060261 to GO:0006367 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0060261
* Added synonym "PAS formation" to GO:0000045
* Changed synonym scope of GO:0000045 from "Related" to "Narrow"
* Deleted GO:0000045 --OBO_REL:is_a--> GO:0006996
* Copied GO:0000045 to GO:0016050 with type OBO_REL:is_a
* Added synonym "perivacuolar space" to GO:0000407
* Changed synonym scope of GO:0000407 from "Related" to "Narrow"
* Deleted general dbxref 2.1.1.73 (EC:<new dbxref>) from synonym site-specific DNA-methyltransferase (cytosine-specific) activity of GO:0003886
* Added general dbxref EC:2.1.1.37 to synonym site-specific DNA-methyltransferase (cytosine-specific) activity of GO:0003886
* Added synonym "vacuolar proteolysis" to GO:0006624
* Changed synonym scope of GO:0006624 from "Related" to "Exact"
* Added synonym "sense organ development" to GO:0007423
* Added general dbxref GOC:dph to synonym sense organ development of GO:0007423
* Changed synonym scope of GO:0007423 from "Related" to "Exact"
* Added synonym "sense organ boundary specification" to GO:0008052
* Added general dbxref GOC:dph to synonym sense organ boundary specification of GO:0008052
* Changed synonym scope of GO:0008052 from "Related" to "Exact"
* added secondary id GO:0034262 to GO:0016236
* Added synonym "autophagy in response to cellular starvation" to GO:0016236
* Changed synonym scope of GO:0016236 from "Related" to "Exact"
* Added synonym "non-specific autophagy" to GO:0016236
* Changed synonym scope of GO:0016236 from "Related" to "Exact"
* Copied GO:0016236 to GO:0009267 with type OBO_REL:is_a
* Added synonym "sense organ precursor cell fate determination" to GO:0016360
* Added general dbxref GOC:dph to synonym sense organ precursor cell fate determination of GO:0016360
* Changed synonym scope of GO:0016360 from "Related" to "Exact"
* Deleted synonym "<new synonym>" from GO:0019988
* Added synonym "cytoplasm-to-vacuole targeting" to GO:0032258
* Changed synonym scope of GO:0032258 from "Related" to "Exact"
* Copied GO:0032258 to GO:0006914 with type part_of
* Deleted GO:0034262 --OBO_REL:is_a--> GO:0009267
* Deleted GO:0034262 --OBO_REL:is_a--> GO:0006914
* Destroyed object GO:0034262
* Changed definition of GO:0034270 from "A receptor-cargo protein complex that is involved in the CVT pathway. In budding yeast, the CVT complex consists of the preApe1p and Atg19p proteins." to "A protein complex that is involved in the CVT pathway. In budding yeast, the CVT complex consists of multimers of preApe1p."
* Deleted synonym "preAPE1-Atg11p complex" from GO:0034270
* Changed definition of GO:0034464 from "A protein complex that associates with the primary cilium and is cilium biogenesis; consists of seven conserved proteins: BBS1, BBS2, BBS4, BBS5, BBS7, BBS8
and BBS9." to "A protein complex that associates with the primary cilium and is cilium biogenesis; consists of seven conserved proteins: BBS1, BBS2, BBS4, BBS5, BBS7, BBS8 and BBS9."
* Changed definition of GO:0034485 from "Catalysis of the reaction: phosphatidylinositol 3,4,5-trisphosphate +
H2O = phosphatidylinositol 3,4-bisphosphate + phosphate." to "Catalysis of the reaction: phosphatidylinositol 3,4,5-trisphosphate + H2O = phosphatidylinositol 3,4-bisphosphate + phosphate."
* Changed definition of GO:0043733 from "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes alkylated purines and pyrimidines by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic or apyrimidinic (AP) site. This enzyme is unable to excise N-7-methylpurines or oxidized bases, such as hypoxanthine." to "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes alkylated 3-methylpurines and pyrimidines by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic or apyrimidinic (AP) site."
* Added general dbxref IMG:00576 to GO:0043733
* Changed definition of GO:0043736 from "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes both N-3- and N-7-methyl purines by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic or apyrimidinic (AP) site." to "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes both N-3- and N-7-methyl purines by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic (AP) site."
* Added general dbxref EC:3.2.2.- to GO:0043736
* Added general dbxref IMG:00578 to GO:0043736
* Added synonym "sense organ precursor cell division" to GO:0045035
* Added general dbxref GOC:dph to synonym sense organ precursor cell division of GO:0045035
* Changed synonym scope of GO:0045035 from "Related" to "Exact"
* Copied GO:0051709 to GO:0043900 with type OBO_REL:is_a
* Copied GO:0051711 to GO:0043901 with type OBO_REL:is_a
* Copied GO:0051712 to GO:0043902 with type OBO_REL:is_a
* Deleted GO:0052330 --part_of--> GO:0051883
* Copied GO:0052330 to GO:0051883 with type positively_regulates

From gocvs at genome.stanford.edu  Wed Jun  4 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Wed, 4 Jun 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 06/04/2008
Message-ID: <200806050430.VAA02782@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.92 by 1.95

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010611
* Created object of type obo:TERM with id GO:0010612
* Created object of type obo:TERM with id GO:0010613
* Created object of type obo:TERM with id GO:0010614
* Created object of type obo:TERM with id GO:0010615
* Created object of type obo:TERM with id GO:0010616
* Created object of type obo:TERM with id GO:0010617
* Created object of type obo:TERM with id GO:0010618
* Created object of type obo:TERM with id GO:0034504
* Populated new object GO:0010611 (macro)
  * Changed name of GO:0010611 from "<new term>" to "regulation of cardiac muscle hypertrophy"
  * Set definition of GO:0010611 to "Any process that modulates the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division."
  * Added definition dbxref GOC:dph to GO:0010611
  * Added definition dbxref GOC:tb to GO:0010611
  * Copied GO:0010611 to GO:0014898 with type regulates
  * Copied GO:0010611 to GO:0010612 with type OBO_REL:is_a
  * Copied GO:0010611 to GO:0014743 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010611
* Populated new object GO:0010612 (macro)
  * Changed name of GO:0010612 from "<new term>" to "regulation of cardiac muscle adaptation"
  * Set definition of GO:0010612 to "Any process that modulates the rate, extent or frequency of the process by which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors."
  * Added definition dbxref GOC:dph to GO:0010612
  * Added definition dbxref GOC:tb to GO:0010612
  * Copied GO:0010612 to GO:0043502 with type OBO_REL:is_a
  * Copied GO:0010612 to GO:0014887 with type regulates
  * Assigned namespace "biological_process" to GO:0010612
* Populated new object GO:0010613 (macro)
  * Changed name of GO:0010613 from "<new term>" to "positive regulation of cardiac muscle hypertrophy"
  * Set definition of GO:0010613 to "Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division."
  * Added definition dbxref GOC:dph to GO:0010613
  * Added definition dbxref GOC:tb to GO:0010613
  * Copied GO:0010613 to GO:0010611 with type OBO_REL:is_a
  * Copied GO:0010613 to GO:0014898 with type positively_regulates
  * Copied GO:0010613 to GO:0014742 with type OBO_REL:is_a
  * Copied GO:0010613 to GO:0010615 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010613
* Populated new object GO:0010614 (macro)
  * Changed name of GO:0010614 from "<new term>" to "negative regulation of cardiac muscle hypertrophy"
  * Set definition of GO:0010614 to "Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division."
  * Added definition dbxref GOC:dph to GO:0010614
  * Added definition dbxref GOC:tb to GO:0010614
  * Copied GO:0010614 to GO:0014898 with type negatively_regulates
  * Copied GO:0010614 to GO:0010616 with type OBO_REL:is_a
  * Copied GO:0010614 to GO:0010611 with type OBO_REL:is_a
  * Copied GO:0010614 to GO:0014741 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010614
* Populated new object GO:0010615 (macro)
  * Changed name of GO:0010615 from "<new term>" to "positive regulation of cardiac muscle adaptation"
  * Set definition of GO:0010615 to "Any process that increases the rate, extent or frequency of the process by which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors."
  * Added definition dbxref GOC:dph to GO:0010615
  * Added definition dbxref GOC:tb to GO:0010615
  * Copied GO:0010615 to GO:0014744 with type OBO_REL:is_a
  * Copied GO:0010615 to GO:0010612 with type OBO_REL:is_a
  * Copied GO:0010615 to GO:0014887 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010615
* Populated new object GO:0010616 (macro)
  * Changed name of GO:0010616 from "<new term>" to "negative regulation of cardiac muscle adaptation"
  * Set definition of GO:0010616 to "Any process that decreases the rate, extent or frequency of the process by which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors."
  * Added definition dbxref GOC:dph to GO:0010616
  * Added definition dbxref GOC:tb to GO:0010616
  * Copied GO:0010616 to GO:0014745 with type OBO_REL:is_a
  * Copied GO:0010616 to GO:0010612 with type OBO_REL:is_a
  * Copied GO:0010616 to GO:0014887 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0010616
* Populated new object GO:0010617 (macro)
  * Changed name of GO:0010617 from "<new term>" to "circadian regulation of calcium ion oscillation"
  * Set definition of GO:0010617 to "Any process that modulates the concentration of cytosolic free calcium ion [Ca2+]cyt with a regularity of approximately 24 hours."
  * Added definition dbxref PMID:17982000 to GO:0010617
  * Added synonym " circadian regulation of Ca2+ oscillation" to GO:0010617
  * Added synonym "circadian regulation of [Ca2+]cyt oscillation" to GO:0010617
  * Added synonym "circadian regulation of cytosolic free calcium ion oscillation" to GO:0010617
  * Copied GO:0010617 to GO:0007623 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010617
* Populated new object GO:0010618 (macro)
  * Changed name of GO:0010618 from "<new term>" to "aerenchyma formation"
  * Set definition of GO:0010618 to "The process that gives rise to aerenchyma, parenchyma tissue containing particularly large intercellular spaces of schizogenous or lysigenous origin. This process pertains to the initial formation of a structure from unspecified parts."
  * Added definition dbxref PMID:18055613 to GO:0010618
  * Added definition dbxref PO:0005702 to GO:0010618
  * Copied GO:0010618 to GO:0048646 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010618
* Populated new object GO:0034504 (macro)
  * Changed name of GO:0034504 from "<new term>" to "protein localization in nucleus"
  * Set definition of GO:0034504 to "A process by which a protein is transported to, or maintained in, a location within the nucleus."
  * Added definition dbxref GOC:ecd to GO:0034504
  * Copied GO:0034504 to GO:0033365 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034504
* Added synonym "RNA polymerase I upstream activation factor complex" to GO:0000500
* Changed synonym scope of GO:0000500 from "Related" to "Exact"
* Copied GO:0002764 to GO:0050776 with type OBO_REL:is_a
* Changed definition of GO:0004143 from "Catalysis of the reaction: ATP + 1,2-diacylglycerol = ADP + 1,2-diacylglycerol 3-phosphate." to "Catalysis of the reaction: NTP + 1,2-diacylglycerol = NDP + 1,2-diacylglycerol 3-phosphate."
* Added definition dbxref GOC:elh to GO:0004143
* Changed synonym scope of GO:0004143 from "Exact" to "Narrow"
* Changed synonym scope of GO:0004143 from "Exact" to "Narrow"
* Changed synonym scope of GO:0004143 from "Exact" to "Narrow"
* Copied GO:0007165 to GO:0050794 with type OBO_REL:is_a
* Changed definition of GO:0016592 from "A multiprotein transcriptional mediator complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and is essential for transcription of most protein-coding genes. The Saccharomyces complex contains a core of core complex consists of 16 polypeptides: Srb2, -4, -5, -6, and -7, Med1, -2, -4, -6, -7, and -8, Gal11, Sin4, Rgr1, Rox3, and Pgd1 proteins; mammalian Srb-mediator complexes include homologs of yeast Srb and Med proteins." to "A multiprotein transcriptional mediator complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and is essential for transcription of most protein-coding genes. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Mammalian Srb-mediator complexes include homologs of yeast Srb and Med proteins."
* Added definition dbxref PMID:16168358 to GO:0016592

From gocvs at genome.stanford.edu  Thu Jun  5 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Thu, 5 Jun 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 06/05/2008
Message-ID: <200806060430.VAA13166@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.95 by 1.98

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0043917
* Created object of type obo:TERM with id GO:0043918
* Populated new object GO:0043917 (macro)
  * Changed name of GO:0043917 from "<new term>" to "ribose 1,5-bisphosphate isomerase activity"
  * Set definition of GO:0043917 to "Catalysis of the reaction: D-ribose 1,5-bisphosphate = D-ribulose 1,5-bisphosphate."
  * Added definition dbxref GOC:jl to GO:0043917
  * Added definition dbxref IMG:03024 to GO:0043917
  * Added general dbxref EC:5.3.1.- to GO:0043917
  * Added general dbxref IMG:03024 to GO:0043917
  * Added GO:0043917 to category gosubset_prok
  * Added synonym "ribose-1,5-bisphosphate isomerase activity" to GO:0043917
  * Changed synonym scope of GO:0043917 from "Related" to "Exact"
  * Copied GO:0043917 to GO:0016861 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043917
* Populated new object GO:0043918 (macro)
  * Changed name of GO:0043918 from "<new term>" to "cadaverine aminopropyltransferase activity"
  * Set definition of GO:0043918 to "Catalysis of the reaction: S-adenosylmethioninamine + cadaverine = 5'-methylthioadenosine + N-(3-aminopropyl)cadaverine."
  * Added definition dbxref GOC:jl to GO:0043918
  * Added definition dbxref IMG:00522 to GO:0043918
  * Added definition dbxref PMID:17545282 to GO:0043918
  * Added general dbxref EC:2.5.1.- to GO:0043918
  * Added general dbxref IMG:00522 to GO:0043918
  * Added GO:0043918 to category gosubset_prok
  * Added synonym "cadaverine aminopropyl transferase activity" to GO:0043918
  * Changed synonym scope of GO:0043918 from "Related" to "Exact"
  * Copied GO:0043918 to GO:0016765 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043918
* Deleted GO:0001894 --OBO_REL:is_a--> GO:0042592
* Copied GO:0002759 to GO:0043900 with type OBO_REL:is_a
* Copied GO:0002760 to GO:0043902 with type OBO_REL:is_a
* Copied GO:0008348 to GO:0043901 with type OBO_REL:is_a
* Copied GO:0010112 to GO:0043900 with type OBO_REL:is_a
* Copied GO:0010113 to GO:0043901 with type OBO_REL:is_a
* Set definition of GO:0016861 to "Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is an aldose or a ketose, are the same molecule, and no oxidized product appears."
* Added definition dbxref GOC:jl to GO:0016861
* Set definition of GO:0016862 to "Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is a keto- or an enol-group, are the same molecule, and no oxidized product appears."
* Added definition dbxref GOC:jl to GO:0016862
* Deleted GO:0030420 --OBO_REL:is_a--> GO:0009294
* Copied GO:0030420 to GO:0031668 with type OBO_REL:is_a
* Copied GO:0030420 to GO:0009294 with type part_of
* Deleted GO:0031135 --OBO_REL:is_a--> GO:0048519
* Copied GO:0031135 to GO:0043901 with type OBO_REL:is_a
* Deleted GO:0031136 --OBO_REL:is_a--> GO:0048518
* Copied GO:0031136 to GO:0043902 with type OBO_REL:is_a
* Deleted GO:0032974 --OBO_REL:is_a--> GO:0007034
* Deleted GO:0033666 --OBO_REL:is_a--> GO:0048518
* Copied GO:0033666 to GO:0043902 with type OBO_REL:is_a
* Deleted GO:0033667 --OBO_REL:is_a--> GO:0048519
* Copied GO:0033667 to GO:0043901 with type OBO_REL:is_a
* Deleted GO:0042786 --OBO_REL:is_a--> GO:0051813
* Deleted GO:0045304 --OBO_REL:is_a--> GO:0050789
* Copied GO:0045304 to GO:0050794 with type OBO_REL:is_a
* Deleted GO:0045808 --OBO_REL:is_a--> GO:0048519
* Copied GO:0045808 to GO:0048523 with type OBO_REL:is_a
* Deleted GO:0045809 --OBO_REL:is_a--> GO:0048518
* Copied GO:0045809 to GO:0048522 with type OBO_REL:is_a
* Deleted GO:0046999 --OBO_REL:is_a--> GO:0050789
* Copied GO:0046999 to GO:0043900 with type OBO_REL:is_a
* Copied GO:0050687 to GO:0043901 with type OBO_REL:is_a
* Copied GO:0050688 to GO:0043900 with type OBO_REL:is_a
* Deleted GO:0051813 --OBO_REL:is_a--> GO:0051810
* Copied GO:0051813 to GO:0042786 with type OBO_REL:is_a
* Copied GO:0052063 to GO:0052509 with type OBO_REL:is_a
* Copied GO:0052064 to GO:0052509 with type OBO_REL:is_a
* Deleted GO:0052068 --OBO_REL:is_a--> GO:0052037
* Copied GO:0052068 to GO:0052562 with type OBO_REL:is_a
* Deleted GO:0052075 --OBO_REL:is_a--> GO:0052509
* Copied GO:0052075 to GO:0052556 with type OBO_REL:is_a
* Copied GO:0052078 to GO:0052037 with type OBO_REL:is_a
* Deleted GO:0052088 --OBO_REL:is_a--> GO:0052031
* Copied GO:0052088 to GO:0052553 with type OBO_REL:is_a
* Copied GO:0052170 to GO:0052562 with type OBO_REL:is_a
* Copied GO:0052230 to GO:0032386 with type OBO_REL:is_a
* Copied GO:0052231 to GO:0050764 with type OBO_REL:is_a
* Copied GO:0052248 to GO:0043067 with type OBO_REL:is_a
* Copied GO:0052255 to GO:0031347 with type OBO_REL:is_a
* Copied GO:0052256 to GO:0050727 with type OBO_REL:is_a
* Copied GO:0052259 to GO:0050729 with type OBO_REL:is_a
* Copied GO:0052260 to GO:0050728 with type OBO_REL:is_a
* Copied GO:0052261 to GO:0031348 with type OBO_REL:is_a
* Copied GO:0052298 to GO:0002831 with type OBO_REL:is_a
* Copied GO:0052298 to GO:0045088 with type OBO_REL:is_a
* Copied GO:0052299 to GO:0010112 with type OBO_REL:is_a
* Copied GO:0052312 to GO:0045449 with type OBO_REL:is_a
* Copied GO:0052433 to GO:0042981 with type OBO_REL:is_a
* Copied GO:0052459 to GO:0043070 with type OBO_REL:is_a
* Copied GO:0052490 to GO:0043069 with type OBO_REL:is_a
* Copied GO:0052501 to GO:0043065 with type OBO_REL:is_a
* Copied GO:0052510 to GO:0031349 with type OBO_REL:is_a
* Copied GO:0052518 to GO:0043071 with type OBO_REL:is_a
* Copied GO:0052522 to GO:0050766 with type OBO_REL:is_a
* Copied GO:0052532 to GO:0052510 with type OBO_REL:is_a
* Copied GO:0052532 to GO:0002833 with type OBO_REL:is_a
* Copied GO:0052532 to GO:0045089 with type OBO_REL:is_a
* Copied GO:0052533 to GO:0052509 with type OBO_REL:is_a
* Copied GO:0052535 to GO:0045089 with type OBO_REL:is_a
* Copied GO:0052535 to GO:0002833 with type OBO_REL:is_a
* Copied GO:0052535 to GO:0052510 with type OBO_REL:is_a
* Copied GO:0052537 to GO:0052509 with type OBO_REL:is_a
* Copied GO:0052552 to GO:0050776 with type OBO_REL:is_a
* Copied GO:0052555 to GO:0050778 with type OBO_REL:is_a
* Copied GO:0052561 to GO:0050777 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Fri Jun  6 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Fri, 6 Jun 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 06/06/2008
Message-ID: <200806070430.VAA18866@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.98 by 1.99

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0060262
* Created object of type obo:TERM with id GO:0060263
* Created object of type obo:TERM with id GO:0060264
* Created object of type obo:TERM with id GO:0060265
* Created object of type obo:TERM with id GO:0060266
* Created object of type obo:TERM with id GO:0060267
* Created object of type obo:TERM with id GO:0060268
* Populated new object GO:0060262 (macro)
  * Changed name of GO:0060262 from "<new term>" to "negative regulation of N-terminal protein palmitoylation"
  * Set definition of GO:0060262 to "Any process that decreases the rate frequency or extent of the covalent or non-covalent attachment of a palmitoyl moiety to the N-terminal amino acid residue of a protein."
  * Added definition dbxref GOC:dph to GO:0060262
  * Added definition dbxref GOC:tb to GO:0060262
  * Copied GO:0060262 to GO:0050748 with type OBO_REL:is_a
  * Copied GO:0060262 to GO:0010558 with type OBO_REL:is_a
  * Copied GO:0060262 to GO:0006500 with type negatively_regulates
  * Copied GO:0060262 to GO:0060254 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060262
* Populated new object GO:0060263 (macro)
  * Changed name of GO:0060263 from "<new term>" to "regulation of respiratory burst"
  * Set definition of GO:0060263 to "Any process that modulates the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals."
  * Added definition dbxref GOC:dph to GO:0060263
  * Added definition dbxref GOC:tb to GO:0060263
  * Copied GO:0060263 to GO:0019222 with type OBO_REL:is_a
  * Copied GO:0060263 to GO:0045730 with type regulates
  * Assigned namespace "biological_process" to GO:0060263
* Populated new object GO:0060264 (macro)
  * Changed name of GO:0060264 from "<new term>" to "regulation of respiratory burst during acute inflammatory response"
  * Set definition of GO:0060264 to "Any process that modulates the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense reponse ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals."
  * Added definition dbxref GOC:dph to GO:0060264
  * Added definition dbxref GOC:rl to GO:0060264
  * Added definition dbxref GOC:tb to GO:0060264
  * Copied GO:0060264 to GO:0002536 with type regulates
  * Copied GO:0060264 to GO:0060263 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060264
* Populated new object GO:0060265 (macro)
  * Changed name of GO:0060265 from "<new term>" to "positive regulation of respiratory burst during acute inflammatory response"
  * Set definition of GO:0060265 to "Any process that increases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense reponse ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals."
  * Added definition dbxref GOC:dph to GO:0060265
  * Added definition dbxref GOC:tb to GO:0060265
  * Copied GO:0060265 to GO:0002536 with type positively_regulates
  * Copied GO:0060265 to GO:0060264 with type OBO_REL:is_a
  * Copied GO:0060265 to GO:0060267 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060265
* Populated new object GO:0060266 (macro)
  * Changed name of GO:0060266 from "<new term>" to "negative regulation of respiratory burst during acute inflammatory response"
  * Set definition of GO:0060266 to "Any process that decreases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense reponse ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals."
  * Added definition dbxref GOC:dph to GO:0060266
  * Added definition dbxref GOC:tb to GO:0060266
  * Copied GO:0060266 to GO:0060264 with type OBO_REL:is_a
  * Copied GO:0060266 to GO:0002536 with type negatively_regulates
  * Copied GO:0060266 to GO:0060268 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060266
* Populated new object GO:0060267 (macro)
  * Changed name of GO:0060267 from "<new term>" to "positive regulation of respiratory burst"
  * Set definition of GO:0060267 to "Any process that increases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals."
  * Added definition dbxref GOC:dph to GO:0060267
  * Added definition dbxref GOC:tb to GO:0060267
  * Copied GO:0060267 to GO:0045730 with type positively_regulates
  * Copied GO:0060267 to GO:0060263 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060267
* Populated new object GO:0060268 (macro)
  * Changed name of GO:0060268 from "<new term>" to "negative regulation of respiratory burst"
  * Set definition of GO:0060268 to "Any process that decreases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals."
  * Added definition dbxref GOC:dph to GO:0060268
  * Added definition dbxref GOC:tb to GO:0060268
  * Copied GO:0060268 to GO:0060263 with type OBO_REL:is_a
  * Copied GO:0060268 to GO:0045730 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0060268
* Copied GO:0004861 to GO:0016538 with type OBO_REL:is_a
* Added synonym "circadian regulation of cytosolic calcium ion homeostasis" to GO:0010617
* Added general dbxref GOC:tb to synonym circadian regulation of cytosolic calcium ion homeostasis of GO:0010617
* Added general dbxref GOC:dph to synonym circadian regulation of cytosolic calcium ion homeostasis of GO:0010617
* Changed synonym scope of GO:0010617 from "Related" to "Exact"
* Copied GO:0010617 to GO:0051480 with type OBO_REL:is_a
* Deleted GO:0045730 --OBO_REL:is_a--> GO:0009893
* Copied GO:0045730 to GO:0008152 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Mon Jun  9 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Mon, 9 Jun 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 06/09/2008
Message-ID: <200806100430.VAA26390@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.99 by 1.101

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010619
* Created object of type obo:TERM with id GO:0010620
* Created object of type obo:TERM with id GO:0010621
* Populated new object GO:0010619 (macro)
  * Changed name of GO:0010619 from "<new term>" to "activation of adenylate cyclase activity involved in G-protein signaling by glucose"
  * Set definition of GO:0010619 to "Any glucose-triggered process that initiates the activity of an inactive adenylate cyclase that is an integral part of the series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, resulting in a subsequent change in the concentration of cyclic AMP."
  * Added definition dbxref GOC:dph to GO:0010619
  * Added definition dbxref GOC:tb to GO:0010619
  * Added synonym "activation of adenylate cyclase activity by glucose involved in G-protein signaling" to GO:0010619
  * Added general dbxref GOC:tb to synonym activation of adenylate cyclase activity by glucose involved in G-protein signaling of GO:0010619
  * Added general dbxref GOC:dph to synonym activation of adenylate cyclase activity by glucose involved in G-protein signaling of GO:0010619
  * Changed synonym scope of GO:0010619 from "Related" to "Exact"
  * Copied GO:0010619 to GO:0010580 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010619
* Populated new object GO:0010620 (macro)
  * Changed name of GO:0010620 from "<new term>" to "negative regulation of transcription by transcription factor catabolism"
  * Set definition of GO:0010620 to "Any process that stops, prevents or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the catabolism of a transcription factor."
  * Added definition dbxref GOC:dph to GO:0010620
  * Added definition dbxref GOC:tb to GO:0010620
  * Copied GO:0010620 to GO:0044257 with type OBO_REL:is_a
  * Copied GO:0010620 to GO:0045892 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010620
* Populated new object GO:0010621 (macro)
  * Changed name of GO:0010621 from "<new term>" to "negative regulation of transcription by transcription factor localization"
  * Set definition of GO:0010621 to "Any process that stops, prevents or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor."
  * Added definition dbxref GOC:dph to GO:0010621
  * Added definition dbxref GOC:tb to GO:0010621
  * Copied GO:0010621 to GO:0045892 with type OBO_REL:is_a
  * Copied GO:0010621 to GO:0008104 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010621
* Changed definition of GO:0043582 from "The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. A sporangium is a plant or fungal structure producing and containing spores." to "The process whose specific outcome is the progression of the sporangium over time, from its formation to the mature structure. A sporangium is a plant or fungal structure producing and containing spores."

From gocvs at genome.stanford.edu  Tue Jun 10 21:30:48 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Tue, 10 Jun 2008 21:30:48 -0700 (PDT)
Subject: [Go-diff] GO update 06/10/2008
Message-ID: <200806110430.VAA21842@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.101 by 1.104

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010622
* Created object of type obo:TERM with id GO:0043919
* Created object of type obo:TERM with id GO:0043920
* Populated new object GO:0010622 (macro)
  * Changed name of GO:0010622 from "<new term>" to "specification of ovule identity"
  * Set definition of GO:0010622 to "The regionalization process by which the identity of an ovule is specified. Identity is considered to be the aggregate of characteristics by which a structure is recognized."
  * Added definition dbxref GOC:tb to GO:0010622
  * Copied GO:0010622 to GO:0048482 with type part_of
  * Copied GO:0010622 to GO:0003002 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010622
* Populated new object GO:0043919 (macro)
  * Changed name of GO:0043919 from "<new term>" to "agmatine aminopropyltransferase activity"
  * Set definition of GO:0043919 to "Catalysis of the reaction: agmatine + S-adenosylmethioninamine = N1-aminopropylagmatine + 5'-methylthioadenosine."
  * Added definition dbxref GOC:jl to GO:0043919
  * Added definition dbxref IMG:03077 to GO:0043919
  * Added definition dbxref PMID:15983049 to GO:0043919
  * Added general dbxref EC:2.5.1.- to GO:0043919
  * Added general dbxref IMG:03077 to GO:0043919
  * Added GO:0043919 to category gosubset_prok
  * Added synonym "agmatine aminopropyl transferase activity" to GO:0043919
  * Changed synonym scope of GO:0043919 from "Related" to "Exact"
  * Copied GO:0043919 to GO:0016765 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043919
* Populated new object GO:0043920 (macro)
  * Changed name of GO:0043920 from "<new term>" to "aminopropylagmatine ureohydrolase activity"
  * Set definition of GO:0043920 to "Catalysis of the reaction: N1-aminopropylagmatine + H2O = spermidine + urea."
  * Added definition dbxref GOC:jl to GO:0043920
  * Added definition dbxref IMG:03079 to GO:0043920
  * Added definition dbxref PMID:15983049 to GO:0043920
  * Added general dbxref EC:3.5.3.- to GO:0043920
  * Added general dbxref IMG:03079 to GO:0043920
  * Added GO:0043920 to category gosubset_prok
  * Copied GO:0043920 to GO:0016813 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043920
* Deleted definition dbxref MGD:ajp from GO:0001668
* Added definition dbxref GOC:ajp to GO:0001668
* Added GO:0008933 to category gosubset_prok
* Added synonym "peptidoglycan lytic transglycosylase activity" to GO:0008933
* Changed synonym scope of GO:0008933 from "Related" to "Exact"
* Added synonym "floral evocation" to GO:0010228
* Added general dbxref DOI:10.1146/annurev.pp.39.060188.001135 to synonym floral evocation of GO:0010228
* Deleted definition dbxref KEGG:C03367 from GO:0051679
* Added definition dbxref LIGAND:C03367 to GO:0051679

From gocvs at genome.stanford.edu  Wed Jun 11 21:30:52 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Wed, 11 Jun 2008 21:30:52 -0700 (PDT)
Subject: [Go-diff] GO update 06/11/2008
Message-ID: <200806120430.VAA12179@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.104 by 1.105

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034505
* Created object of type obo:TERM with id GO:0034506
* Created object of type obo:TERM with id GO:0034507
* Created object of type obo:TERM with id GO:0034508
* Created object of type obo:TERM with id GO:0034509
* Populated new object GO:0034505 (macro)
  * Changed name of GO:0034505 from "<new term>" to "tooth mineralization"
  * Set definition of GO:0034505 to "The process by which calcium salts are deposited into calcareous tooth structure such as dental enamel, dentin and cementum."
  * Added definition dbxref GOC:mah to GO:0034505
  * Added definition dbxref MESH:tooth+calcification to GO:0034505
  * Added definition dbxref MP:0002817 to GO:0034505
  * Added synonym "tooth calcification" to GO:0034505
  * Changed synonym scope of GO:0034505 from "Related" to "Exact"
  * Copied GO:0034505 to GO:0042476 with type part_of
  * Copied GO:0034505 to GO:0031214 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034505
* Populated new object GO:0034506 (macro)
  * Changed name of GO:0034506 from "<new term>" to "chromosome, centromeric core region"
  * Set definition of GO:0034506 to "The innermost portion of the centromeric region of a chromosome, encompassing the core region of a chromosome centromere and the proteins that bind to it."
  * Added definition dbxref GOC:mah to GO:0034506
  * Added definition dbxref GOC:val to GO:0034506
  * Added synonym "chromosome, centric core region" to GO:0034506
  * Copied GO:0034506 to GO:0000775 with type part_of
  * Copied GO:0034506 to GO:0044427 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034506
* Populated new object GO:0034507 (macro)
  * Changed name of GO:0034507 from "<new term>" to "chromosome, centromeric outer repeat region"
  * Set definition of GO:0034507 to "The portion of the centromeric region of a chromosome that flanks the core region, encompassing repeated regions of a chromosome centromere and the proteins that bind to it."
  * Added definition dbxref GOC:mah to GO:0034507
  * Added definition dbxref GOC:val to GO:0034507
  * Added synonym "chromosome, centric outer repeat region" to GO:0034507
  * Copied GO:0034507 to GO:0000775 with type part_of
  * Copied GO:0034507 to GO:0044427 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034507
* Populated new object GO:0034508 (macro)
  * Changed name of GO:0034508 from "<new term>" to "centromere complex assembly"
  * Set definition of GO:0034508 to "The aggregation, arrangement and bonding together of proteins and centromeric DNA molecules to form a centromeric protein-DNA complex. Includes the formation of the chromatin structures which form a platform for the kinetochore, and assembly of the kinetochore onto this specialzed chromatin. In fission yeast and higher eukaryotes this process also includes the formation of heterochromatin at the outer repeat (pericentric) regions of the centromere."
  * Added definition dbxref GOC:mah to GO:0034508
  * Added definition dbxref GOC:vw to GO:0034508
  * Copied GO:0034508 to GO:0051276 with type OBO_REL:is_a
  * Copied GO:0034508 to GO:0065004 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034508
* Populated new object GO:0034509 (macro)
  * Changed name of GO:0034509 from "<new term>" to "centromeric core chromatin formation"
  * Set definition of GO:0034509 to "The assembly of chromatin into the specialized structure characteristic of the centromeric core region, defined by the presence of the variant histone CENP-A."
  * Added definition dbxref GOC:mah to GO:0034509
  * Added definition dbxref GOC:vw to GO:0034509
  * Added synonym "centric core chromatin formation" to GO:0034509
  * Changed synonym scope of GO:0034509 from "Related" to "Exact"
  * Added synonym "centromeric core chromatin assembly" to GO:0034509
  * Changed synonym scope of GO:0034509 from "Related" to "Exact"
  * Copied GO:0034509 to GO:0031497 with type OBO_REL:is_a
  * Copied GO:0034509 to GO:0034508 with type part_of
  * Assigned namespace "biological_process" to GO:0034509
* Changed synonym scope of GO:0000500 from "Broad" to "Exact"
* Changed name of GO:0000775 from "chromosome, pericentric region" to "chromosome, centromeric region"
* Changed definition of GO:0000775 from "The central region of a chromosome that includes the centromere and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." to "The region of a chromosome that includes the centromere and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome."
* Added synonym "chromosome, centric region" to GO:0000775
* Changed synonym scope of GO:0000775 from "Related" to "Exact"
* Added synonym "chromosome, pericentric region" to GO:0000775
* Changed definition of GO:0000776 from "A multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules." to "A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules."
* Changed definition of GO:0000777 from "A multisubunit complex that is located at the pericentric region of a condensed chromosome and provides an attachment point for the spindle microtubules." to "A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules."
* Changed definition of GO:0000778 from "A multisubunit complex that is located at the pericentric region of a condensed chromosome in the nucleus and provides an attachment point for the spindle microtubules." to "A multisubunit complex that is located at the centromeric region of a condensed chromosome in the nucleus and provides an attachment point for the spindle microtubules."
* Changed name of GO:0000779 from "condensed chromosome, pericentric region" to "condensed chromosome, centromeric region"
* Changed definition of GO:0000779 from "The central region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." to "The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome."
* Added synonym "condensed chromosome, centric region" to GO:0000779
* Changed synonym scope of GO:0000779 from "Related" to "Exact"
* Added synonym "condensed chromosome, pericentric region" to GO:0000779
* Changed name of GO:0000780 from "condensed nuclear chromosome, pericentric region" to "condensed nuclear chromosome, centromeric region"
* Changed definition of GO:0000780 from "The central region of a condensed chromosome in the nucleus that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." to "The region of a condensed chromosome in the nucleus that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome."
* Added synonym "condensed nuclear chromosome, centric region" to GO:0000780
* Changed synonym scope of GO:0000780 from "Related" to "Exact"
* Added synonym "condensed nuclear chromosome, pericentric region" to GO:0000780
* Added synonym "CTP:diacylglycerol kinase activity" to GO:0004143
* Changed synonym scope of GO:0004143 from "Related" to "Narrow"
* Changed name of GO:0005721 from "centric heterochromatin" to "centromeric heterochromatin"
* Deleted synonym "centromeric heterochromatin" from GO:0005721
* Added synonym "centric heterochromatin" to GO:0005721
* Changed synonym scope of GO:0005721 from "Related" to "Exact"
* Copied GO:0006260 to GO:0043284 with type OBO_REL:is_a
* Added synonym "RNA-protein complex biogenesis and assembly" to GO:0022613
* Changed synonym scope of GO:0022613 from "Related" to "Exact"
* Added synonym "biomineralization" to GO:0031214
* Changed synonym scope of GO:0031214 from "Related" to "Exact"
* Changed name of GO:0031508 from "centric heterochromatin formation" to "centromeric heterochromatin formation"
* Deleted synonym "centric heterochromatin assembly" from GO:0031508
* Deleted synonym "centromeric heterochromatin formation" from GO:0031508
* Added synonym "centric heterochromatin formation" to GO:0031508
* Changed synonym scope of GO:0031508 from "Related" to "Exact"
* Added synonym "centromeric heterochromatin assembly" to GO:0031508
* Changed synonym scope of GO:0031508 from "Related" to "Exact"
* Copied GO:0031508 to GO:0034508 with type part_of
* Changed name of GO:0031618 from "nuclear centric heterochromatin" to "nuclear centromeric heterochromatin"
* Added synonym "nuclear centric heterochromatin" to GO:0031618
* Changed synonym scope of GO:0031618 from "Related" to "Exact"
* Deleted GO:0032040 --OBO_REL:is_a--> GO:0030529
* Deleted GO:0032040 --OBO_REL:is_a--> GO:0044452
* Copied GO:0032040 to GO:0030685 with type OBO_REL:is_a
* Changed name of GO:0042475 from "odontogenesis of dentine-containing teeth" to "odontogenesis of dentine-containing tooth"
* Changed definition of GO:0042475 from "The process whose specific outcome is the progression of a tooth over time, from its formation to the mature structure. Teeth are the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates, and which usually aid in the prehension and mastication of food." to "The process whose specific outcome is the progression of a dentine-containing tooth over time, from its formation to the mature structure. A dentine-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and are composed mainly of dentine, a dense calcified substance, covered by a layer of enamel."
* Deleted definition dbxref GOC:jl from GO:0042475
* Deleted definition dbxref MetaCyc:THRESYN-PWY from GO:0042475
* Added definition dbxref GOC:mah to GO:0042475
* Added definition dbxref PMID:10333884 to GO:0042475
* Added synonym "odontogenesis of dentine-containing teeth" to GO:0042475
* Changed synonym scope of GO:0042475 from "Related" to "Exact"
* added secondary id GO:0042477 to GO:0042476
* Changed definition of GO:0042476 from "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s)." to "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food."
* Added definition dbxref GOC:mah to GO:0042476
* Added synonym "odontogenesis (sensu Protostomia)" to GO:0042476
* Changed synonym scope of GO:0042476 from "Related" to "Narrow"
* Added synonym "odontogenesis of calcareous or chitinous tooth" to GO:0042476
* Changed synonym scope of GO:0042476 from "Related" to "Narrow"
* Added synonym "tooth development (sensu Invertebrata)" to GO:0042476
* Changed synonym scope of GO:0042476 from "Related" to "Narrow"
* Deleted GO:0042477 --OBO_REL:is_a--> GO:0042476
* Deleted GO:0042484 --regulates--> GO:0042477
* Deleted GO:0042485 --positively_regulates--> GO:0042477
* Deleted GO:0042486 --negatively_regulates--> GO:0042477
* Destroyed object GO:0042477
* added secondary id GO:0042484 to GO:0042481
* Added synonym "regulation of odontogenesis (sensu Protostomia)" to GO:0042481
* Changed synonym scope of GO:0042481 from "Related" to "Narrow"
* Added synonym "regulation of odontogenesis of calcareous or chitinous tooth" to GO:0042481
* Changed synonym scope of GO:0042481 from "Related" to "Narrow"
* Added synonym "regulation of tooth development" to GO:0042481
* Changed synonym scope of GO:0042481 from "Related" to "Exact"
* added secondary id GO:0042485 to GO:0042482
* Added synonym "activation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "positive regulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Exact"
* Added synonym "positive regulation of odontogenesis of calcareous or chitinous tooth" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "positive regulation of tooth development" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Exact"
* Added synonym "stimulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "up regulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "up-regulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "upregulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* added secondary id GO:0042486 to GO:0042483
* Added synonym "down regulation of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "down-regulation of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "downregulation of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "inhibition of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "negative regulation of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "negative regulation of odontogenesis of calcareous or chitinous tooth" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "negative regulation of tooth development" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Exact"
* Deleted GO:0042484 --regulates--> GO:0042477
* Deleted GO:0042484 --OBO_REL:is_a--> GO:0042481
* Deleted GO:0042486 --OBO_REL:is_a--> GO:0042484
* Deleted GO:0042485 --OBO_REL:is_a--> GO:0042484
* Destroyed object GO:0042484
* Deleted GO:0042485 --OBO_REL:is_a--> GO:0042482
* Deleted GO:0042485 --positively_regulates--> GO:0042477
* Deleted GO:0042485 --OBO_REL:is_a--> GO:0042484
* Destroyed object GO:0042485
* Deleted GO:0042486 --OBO_REL:is_a--> GO:0042484
* Deleted GO:0042486 --OBO_REL:is_a--> GO:0042483
* Deleted GO:0042486 --negatively_regulates--> GO:0042477
* Destroyed object GO:0042486
* Changed name of GO:0042487 from "regulation of odontogenesis of dentine-containing teeth" to "regulation of odontogenesis of dentine-containing tooth"
* Added synonym "regulation of odontogenesis of dentine-containing teeth" to GO:0042487
* Changed synonym scope of GO:0042487 from "Related" to "Exact"
* Changed name of GO:0042488 from "positive regulation of odontogenesis of dentine-containing teeth" to "positive regulation of odontogenesis of dentine-containing tooth"
* Added synonym "positive regulation of odontogenesis of dentine-containing teeth" to GO:0042488
* Changed synonym scope of GO:0042488 from "Related" to "Exact"
* Changed name of GO:0042489 from "negative regulation of odontogenesis of dentine-containing teeth" to "negative regulation of odontogenesis of dentine-containing tooth"
* Added synonym "negative regulation of odontogenesis of dentine-containing teeth" to GO:0042489
* Changed synonym scope of GO:0042489 from "Related" to "Exact"
* Changed definition of GO:0051382 from "The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules." to "The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules."
* Copied GO:0051382 to GO:0034508 with type part_of
* Changed definition of GO:0051383 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the kinetochore, a multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules."

From gocvs at genome.stanford.edu  Thu Jun 12 21:30:49 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Thu, 12 Jun 2008 21:30:49 -0700 (PDT)
Subject: [Go-diff] GO update 06/12/2008
Message-ID: <200806130430.VAA02579@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.105 by 1.106

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory

From gocvs at genome.stanford.edu  Fri Jun 13 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Fri, 13 Jun 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 06/13/2008
Message-ID: <200806140430.VAA11961@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.106 by 1.108

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034510
* Created object of type obo:TERM with id GO:0034511
* Created object of type obo:TERM with id GO:0034512
* Created object of type obo:TERM with id GO:0034513
* Created object of type obo:TERM with id GO:0034514
* Populated new object GO:0034510 (macro)
  * Changed name of GO:0034510 from "<new term>" to "centromere separation"
  * Set definition of GO:0034510 to "The cell cycle process whereby centromeres are physically detached from each other during chromosome separation."
  * Added definition dbxref GOC:mah to GO:0034510
  * Copied GO:0034510 to GO:0051304 with type part_of
  * Copied GO:0034510 to GO:0022402 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034510
* Populated new object GO:0034511 (macro)
  * Changed name of GO:0034511 from "<new term>" to "U3 snoRNA binding"
  * Set definition of GO:0034511 to "Interacting selectively with U3 small nucleolar RNA."
  * Added definition dbxref GOC:mah to GO:0034511
  * Copied GO:0034511 to GO:0030515 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034511
* Populated new object GO:0034512 (macro)
  * Changed name of GO:0034512 from "<new term>" to "box C/D snoRNA binding"
  * Set definition of GO:0034512 to "Interacting selectively with box C/D small nucleolar RNA."
  * Added definition dbxref GOC:mah to GO:0034512
  * Copied GO:0034512 to GO:0030515 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034512
* Populated new object GO:0034513 (macro)
  * Changed name of GO:0034513 from "<new term>" to "box H/ACA snoRNA binding"
  * Set definition of GO:0034513 to "Interacting selectively with box H/ACA small nucleolar RNA."
  * Added definition dbxref GOC:mah to GO:0034513
  * Copied GO:0034513 to GO:0030515 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034513
* Populated new object GO:0034514 (macro)
  * Changed name of GO:0034514 from "<new term>" to "mitochondrial unfolded protein response"
  * Set definition of GO:0034514 to "The series of molecular signals generated as a consequence of the presence of unfolded proteins in the mitochondrial matrix; results in transcriptional upregulation of nuclear genes encoding mitochondrial stress proteins."
  * Added definition dbxref GOC:mah to GO:0034514
  * Added definition dbxref PMID:17849004 to GO:0034514
  * Added synonym "mtUPR" to GO:0034514
  * Changed synonym scope of GO:0034514 from "Related" to "Exact"
  * Copied GO:0034514 to GO:0006986 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034514
* Changed definition of GO:0000148 from "The complex that catalyzes the transfer of a glucose moiety from UDP-glucose to a 1,3-beta-D-glucan chain." to "A protein complex that catalyzes the transfer of a glucose moiety from UDP-glucose to a 1,3-beta-D-glucan chain."
* Deleted GO:0000243 --OBO_REL:is_a--> GO:0043234
* Copied GO:0000243 to GO:0030529 with type OBO_REL:is_a
* Deleted definition dbxref IUPHAR:2.1 from GO:0001584
* Added definition dbxref IUPHAR_GPCR:1505 to GO:0001584
* Deleted definition dbxref IUPHAR:2.1 DA 5 from GO:0001589
* Added definition dbxref IUPHAR_RECEPTOR:2260 to GO:0001589
* Deleted definition dbxref IUPHAR:21. DA 1 from GO:0001590
* Added definition dbxref IUPHAR_RECEPTOR:2252 to GO:0001590
* Deleted definition dbxref IUPHAR:2.1 DA 3 from GO:0001592
* Added definition dbxref IUPHAR_RECEPTOR:2256 to GO:0001592
* Deleted definition dbxref IUPHAR:2.1 DA 4 from GO:0001593
* Added definition dbxref IUPHAR_RECEPTOR:2258 to GO:0001593
* Deleted definition dbxref IUPHAR:2.1 ET ETA from GO:0001599
* Added definition dbxref IUPHAR_RECEPTOR:2263 to GO:0001599
* Deleted definition dbxref IUPHAR:2.1 ET ETAB from GO:0001600
* Added definition dbxref IUPHAR_RECEPTOR:2265 to GO:0001600
* Deleted definition dbxref IUPHAR:2.1.NUCT from GO:0001608
* Added definition dbxref IUPHAR_GPCR:1294 to GO:0001608
* Deleted definition dbxref IUPHAR:2.2 from GO:0001633
* Added definition dbxref IUPHAR_GPCR:1506 to GO:0001633
* Deleted definition dbxref IUPHAR:2.1 DA 2 from GO:0001670
* Added definition dbxref IUPHAR_RECEPTOR:2254 to GO:0001670
* Deleted definition dbxref IUPHAR:2.0 from GO:0004930
* Added definition dbxref http://www.iuphar-db.org to GO:0004930
* Deleted definition dbxref IUPHAR:2.1.CBD from GO:0004949
* Added definition dbxref IUPHAR_GPCR:1279 to GO:0004949
* Deleted definition dbxref IUPHAR:2.1 CHK from GO:0004950
* Added definition dbxref IUPHAR_GPCR:1280 to GO:0004950
* Deleted definition dbxref IUPHAR:2.1 DA from GO:0004952
* Added definition dbxref IUPHAR_GPCR:1282 to GO:0004952
* Deleted definition dbxref IUPHAR:2.1 ET from GO:0004962
* Added definition dbxref IUPHAR_GPCR:1283 to GO:0004962
* Deleted definition dbxref IUPHAR:2.3 GLU from GO:0004965
* Added definition dbxref IUPHAR_RECEPTOR:1276 to GO:0004965
* Deleted GO:0005656 --OBO_REL:is_a--> GO:0043234
* Copied GO:0005656 to GO:0032993 with type OBO_REL:is_a
* Deleted definition dbxref IUPHAR:2.3 GLU from GO:0008067
* Added definition dbxref IUPHAR_GPCR:1285 to GO:0008067
* Changed definition of GO:0009377 from "A protein complex that possesses ATP-dependent protease activity; as characterized in E. coli, the complex contains six identical subunits of both ClpY and ClpQ that self-assemble into an oligomeric ring, and two rings of each subunit, two ClpQ rings surrounded by single ClpY rings, to form a dumbbell shape complex." to "Catalysis of the ATP-dependent hydrolysis of peptide bonds in substrates including E. coli SulA and misfolded proteins."
* Deleted definition dbxref PMID:12670962 from GO:0009377
* Added definition dbxref PMID:10368141 to GO:0009377
* Deleted GO:0015935 --OBO_REL:is_a--> GO:0043234
* Set definition of GO:0015985 to "The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that provides energy for the synthesis of ATP or GTP."
* Added definition dbxref GOC:mah to GO:0015985
* Copied GO:0015985 to GO:0034220 with type OBO_REL:is_a
* Set definition of GO:0015988 to "The transport of protons against an electrochemical gradient, using energy from a source such as ATP hydrolysis, light, or electron transport."
* Added definition dbxref GOC:mah to GO:0015988
* Set definition of GO:0015989 to "The transport of protons against an electrochemical gradient, using energy from light."
* Added definition dbxref GOC:mah to GO:0015989
* Set definition of GO:0015990 to "The transport of protons against an electrochemical gradient, using energy from electron transport."
* Added definition dbxref GOC:mah to GO:0015990
* Set definition of GO:0015991 to "The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis."
* Added definition dbxref GOC:mah to GO:0015991
* Deleted GO:0016282 --OBO_REL:is_a--> GO:0043234
* Copied GO:0016282 to GO:0030529 with type OBO_REL:is_a
* Changed definition of GO:0030386 from "Complex that possesses ferredoxin:thioredoxin reductase activity." to "A protein complex that possesses ferredoxin:thioredoxin reductase activity."
* Deleted GO:0030894 --OBO_REL:is_a--> GO:0043234
* Copied GO:0030894 to GO:0032993 with type OBO_REL:is_a
* Changed name of GO:0030968 from "unfolded protein response" to "endoplasmic reticulum unfolded protein response"
* Deleted synonym "UPR" from GO:0030968
* Added synonym "ER unfolded protein response" to GO:0030968
* Changed synonym scope of GO:0030968 from "Related" to "Exact"
* Added synonym "erUPR" to GO:0030968
* Changed synonym scope of GO:0030968 from "Related" to "Exact"
* Deleted GO:0031261 --OBO_REL:is_a--> GO:0043234
* Copied GO:0031261 to GO:0032993 with type OBO_REL:is_a
* Deleted GO:0031421 --OBO_REL:is_a--> GO:0043234
* Copied GO:0031421 to GO:0032993 with type OBO_REL:is_a
* Deleted GO:0033290 --OBO_REL:is_a--> GO:0043234
* Copied GO:0033290 to GO:0030529 with type OBO_REL:is_a
* Deleted GO:0033291 --OBO_REL:is_a--> GO:0043234
* Copied GO:0033291 to GO:0030529 with type OBO_REL:is_a
* Changed definition of GO:0034220 from "The process whereby an ion is transported from one side of a membrane to the other." to "A process whereby an ion is transported from one side of a membrane to the other."
* Deleted GO:0034500 --OBO_REL:is_a--> GO:0051304
* Copied GO:0034500 to GO:0051304 with type part_of
* Copied GO:0034500 to GO:0022402 with type OBO_REL:is_a
* Changed definition of GO:0043234 from "Any protein group composed of two or more subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups." to "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups."
* Added synonym "protein-protein complex" to GO:0043234
* Changed synonym scope of GO:0043234 from "Related" to "Exact"
* Deleted GO:0043614 --OBO_REL:is_a--> GO:0043234
* Copied GO:0043614 to GO:0030529 with type OBO_REL:is_a
* Changed name of GO:0043769 from "telomere binding complex" to "Tpg-containing telomere binding complex"
* Changed definition of GO:0043769 from "A complex composed of four polypeptides: a telomere-protecting terminal protein (Tpg), a telomere-associated protein (Tap), DNA polymerase (PolA) and topoisomerase I (TopA) that functions in the replication of the telomeric regions of linear chromosomes, plasmids and circular replicons of some bacterial species." to "A complex composed of four polypeptides, a telomere-protecting terminal protein (Tpg), a telomere-associated protein (Tap), DNA polymerase (PolA) and topoisomerase I (TopA), that functions in the replication of the telomeric regions of linear chromosomes, plasmids and circular replicons of some bacterial species."
* Changed synonym scope of GO:0043769 from "Exact" to "Broad"
* Deleted GO:0043769 --OBO_REL:is_a--> GO:0044427
* Copied GO:0043769 to GO:0000782 with type OBO_REL:is_a
* Changed name of GO:0043845 from "DNA polymerase III, proof-reading complex" to "DNA polymerase III, proofreading complex"
* Added synonym "DNA polymerase III, proof-reading complex" to GO:0043845
* Changed synonym scope of GO:0043845 from "Related" to "Exact"
* Deleted general dbxref EC:4.1.3 from GO:0043904
* Added general dbxref EC:4.1.3.- to GO:0043904
* Deleted GO:0051756 --OBO_REL:is_a--> GO:0022402
* Copied GO:0051756 to GO:0034510 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Mon Jun 16 21:30:48 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Mon, 16 Jun 2008 21:30:48 -0700 (PDT)
Subject: [Go-diff] GO update 06/16/2008
Message-ID: <200806170430.VAA09975@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.108 by 1.111

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0043921
* Created object of type obo:TERM with id GO:0043922
* Created object of type obo:TERM with id GO:0043923
* Created object of type obo:TERM with id GO:0043924
* Populated new object GO:0043921 (macro)
  * Changed name of GO:0043921 from "<new term>" to "modulation by host of viral transcription"
  * Set definition of GO:0043921 to "Any process by which a host organism modulates the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA."
  * Added definition dbxref GOC:jl to GO:0043921
  * Added synonym "regulation by host of viral transcription" to GO:0043921
  * Changed synonym scope of GO:0043921 from "Related" to "Exact"
  * Added synonym "regulation of viral transcription by host " to GO:0043921
  * Changed synonym scope of GO:0043921 from "Related" to "Exact"
  * Copied GO:0043921 to GO:0052472 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043921
* Populated new object GO:0043922 (macro)
  * Changed name of GO:0043922 from "<new term>" to "negative regulation by host of viral transcription"
  * Set definition of GO:0043922 to "Any process by which a host organism stops, prevents or reduces the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA."
  * Added definition dbxref GOC:jl to GO:0043922
  * Added synonym "negative regulation of viral transcription by host" to GO:0043922
  * Changed synonym scope of GO:0043922 from "Related" to "Exact"
  * Copied GO:0043922 to GO:0016481 with type OBO_REL:is_a
  * Copied GO:0043922 to GO:0043921 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043922
* Populated new object GO:0043923 (macro)
  * Changed name of GO:0043923 from "<new term>" to "positive regulation by host of viral transcription"
  * Set definition of GO:0043923 to "Any process by which a host organism activates or increases the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA."
  * Added definition dbxref GOC:jl to GO:0043923
  * Added synonym "positive regulation of viral transcription by host" to GO:0043923
  * Changed synonym scope of GO:0043923 from "Related" to "Exact"
  * Copied GO:0043923 to GO:0043921 with type OBO_REL:is_a
  * Copied GO:0043923 to GO:0045941 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043923
* Populated new object GO:0043924 (macro)
  * Changed name of GO:0043924 from "<new term>" to "suramin binding"
  * Set definition of GO:0043924 to "Interacting selectively with suramin, a naphthalenesulfonic acid compound which is used in the treatment of diseases caused by trypanosomes and worms."
  * Added definition dbxref CHEBI:45906 to GO:0043924
  * Added definition dbxref GOC:jl to GO:0043924
  * Added definition dbxref http://en.wikipedia.org/wiki/Suramin to GO:0043924
  * Added synonym "Germanin binding" to GO:0043924
  * Changed synonym scope of GO:0043924 from "Related" to "Exact"
  * Copied GO:0043924 to GO:0005488 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043924
* Copied GO:0000960 to GO:0031329 with type OBO_REL:is_a
* Copied GO:0000961 to GO:0031330 with type OBO_REL:is_a
* Copied GO:0000961 to GO:0051253 with type OBO_REL:is_a
* Copied GO:0000962 to GO:0051254 with type OBO_REL:is_a
* Copied GO:0000962 to GO:0031331 with type OBO_REL:is_a
* Deleted GO:0005963 --OBO_REL:is_a--> GO:0043234
* Copied GO:0005963 to GO:0008287 with type OBO_REL:is_a
* Deleted GO:0009117 --OBO_REL:is_a--> GO:0034404
* Copied GO:0016481 to GO:0010558 with type OBO_REL:is_a
* Added synonym "oxo-acid lyase activity" to GO:0016833
* Changed synonym scope of GO:0016833 from "Related" to "Exact"
* Added synonym "oxoacid lyase activity" to GO:0016833
* Changed synonym scope of GO:0016833 from "Related" to "Exact"
* Deleted GO:0017059 --OBO_REL:is_a--> GO:0043234
* Copied GO:0017059 to GO:0031211 with type OBO_REL:is_a
* Changed name of GO:0019056 from "modification by virus of host cell transcription" to "modulation by virus of host transcription"
* Added synonym "modification by virus of host transcription" to GO:0019056
* Changed synonym scope of GO:0019056 from "Related" to "Exact"
* Copied GO:0019056 to GO:0052026 with type OBO_REL:is_a
* Changed definition of GO:0019057 from "The modulation of transcription of cellular protein-coding genes by host RNA polymerase II." to "Any process by which a virus modulates the frequency, rate or extent of translation of host mRNA."
* Copied GO:0033668 to GO:0043066 with type OBO_REL:is_a
* Deleted GO:0042996 --OBO_REL:is_a--> GO:0032386
* Copied GO:0042996 to GO:0033157 with type OBO_REL:is_a
* Copied GO:0042997 to GO:0051224 with type OBO_REL:is_a
* Copied GO:0042998 to GO:0051222 with type OBO_REL:is_a
* Copied GO:0043301 to GO:0051048 with type OBO_REL:is_a
* Copied GO:0043302 to GO:0051047 with type OBO_REL:is_a
* Copied GO:0045449 to GO:0010556 with type OBO_REL:is_a
* Copied GO:0045941 to GO:0010557 with type OBO_REL:is_a
* Deleted GO:0051701 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051701 to GO:0044403 with type part_of
* Copied GO:0051701 to GO:0044419 with type OBO_REL:is_a
* Deleted GO:0051702 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051702 to GO:0044403 with type part_of
* Copied GO:0051702 to GO:0044419 with type OBO_REL:is_a
* Deleted GO:0051708 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051708 to GO:0044403 with type part_of
* Copied GO:0051708 to GO:0044419 with type OBO_REL:is_a
* Deleted GO:0051816 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051816 to GO:0044419 with type OBO_REL:is_a
* Copied GO:0051816 to GO:0044403 with type part_of
* Deleted GO:0051817 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051817 to GO:0044403 with type part_of
* Copied GO:0051817 to GO:0044419 with type OBO_REL:is_a
* Deleted GO:0051821 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051821 to GO:0044403 with type part_of
* Copied GO:0051821 to GO:0044419 with type OBO_REL:is_a
* Deleted GO:0051824 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051824 to GO:0044403 with type part_of
* Copied GO:0051824 to GO:0044419 with type OBO_REL:is_a
* Deleted GO:0051825 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051825 to GO:0044419 with type OBO_REL:is_a
* Copied GO:0051825 to GO:0044403 with type part_of
* Deleted GO:0051836 --OBO_REL:is_a--> GO:0044403
* Copied GO:0051836 to GO:0044419 with type OBO_REL:is_a
* Copied GO:0051836 to GO:0044403 with type part_of
* Deleted GO:0052047 --OBO_REL:is_a--> GO:0044403
* Copied GO:0052047 to GO:0044419 with type OBO_REL:is_a
* Copied GO:0052047 to GO:0044403 with type part_of
* Deleted GO:0052108 --OBO_REL:is_a--> GO:0051701
* Copied GO:0052108 to GO:0051701 with type part_of
* Deleted GO:0052171 --OBO_REL:is_a--> GO:0044403
* Copied GO:0052171 to GO:0044403 with type part_of
* Copied GO:0052171 to GO:0044419 with type OBO_REL:is_a
* Deleted GO:0052173 --OBO_REL:is_a--> GO:0044403
* Copied GO:0052173 to GO:0044419 with type OBO_REL:is_a
* Copied GO:0052173 to GO:0044403 with type part_of
* Deleted GO:0052192 --OBO_REL:is_a--> GO:0044403
* Copied GO:0052192 to GO:0044403 with type part_of
* Copied GO:0052192 to GO:0044419 with type OBO_REL:is_a
* Deleted GO:0055117 --OBO_REL:is_a--> GO:0006937
* Copied GO:0055117 to GO:0006942 with type OBO_REL:is_a
* Deleted GO:0055118 --OBO_REL:is_a--> GO:0055117
* Copied GO:0055118 to GO:0045988 with type OBO_REL:is_a
* Copied GO:0060211 to GO:0031329 with type OBO_REL:is_a
* Copied GO:0060212 to GO:0031330 with type OBO_REL:is_a
* Copied GO:0060213 to GO:0031331 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Tue Jun 17 21:30:48 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Tue, 17 Jun 2008 21:30:48 -0700 (PDT)
Subject: [Go-diff] GO update 06/17/2008
Message-ID: <200806180430.VAA04467@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.111 by 1.112

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Added general dbxref UM-BBD_enzymeID:e0633 to GO:0000334
* Added synonym "cardiac jogging" to GO:0001947
* Changed synonym scope of GO:0001947 from "Related" to "Exact"
* Deleted GO:0003848 --OBO_REL:is_a--> GO:0016301
* Added general dbxref UM-BBD_enzymeID:e0664 to GO:0003857
* Added general dbxref UM-BBD_enzymeID:e0202 to GO:0003955
* Added general dbxref UM-BBD_enzymeID:e0523 to GO:0003959
* Added general dbxref UM-BBD_enzymeID:e0653 to GO:0003988
* Added general dbxref UM-BBD_enzymeID:e0534 to GO:0004039
* Added general dbxref UM-BBD_enzymeID:e0535 to GO:0004064
* Added general dbxref UM-BBD_enzymeID:e0631 to GO:0004091
* Added general dbxref UM-BBD_enzymeID:e0834 to GO:0004096
* Added general dbxref UM-BBD_enzymeID:e0575 to GO:0004494
* Deleted GO:0004749 --OBO_REL:is_a--> GO:0019200
* Added general dbxref UM-BBD_enzymeID:e0509 to GO:0004756
* Deleted GO:0004788 --OBO_REL:is_a--> GO:0016301
* Added general dbxref UM-BBD_enzymeID:e0832 to GO:0004846
* Added general dbxref UM-BBD_enzymeID:e0781 to GO:0004855
* Added synonym "arthropod blood cell development" to GO:0007516
* Changed synonym scope of GO:0007516 from "Related" to "Exact"
* Added general dbxref UM-BBD_enzymeID:e0559 to GO:0008127
* Changed definition of GO:0008467 from "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate, with a substrate consensus sequence of Glc(N2S>NAc)?6S GlcA GlcN2S*?6S GlcA>IdoA?2S Glc(N2S/NAc)?6S." to "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate, with a substrate consensus sequence of Glc(N2S>NAc)+/-6S GlcA GlcN2S*?6S GlcA>IdoA+/-2S Glc(N2S/NAc)+/-6S."
* Added general dbxref UM-BBD_enzymeID:e0077 to GO:0008701
* Deleted GO:0008728 --OBO_REL:is_a--> GO:0019205
* Added general dbxref UM-BBD_enzymeID:e0711 to GO:0009821
* Changed name of GO:0016791 from "phosphoric monoester hydrolase activity" to "phosphatase activity"
* Deleted synonym "phosphatase activity" from GO:0016791
* Added synonym "phosphoric monoester hydrolase activity" to GO:0016791
* Changed synonym scope of GO:0016791 from "Related" to "Exact"
* Added general dbxref UM-BBD_enzymeID:e0808 to GO:0016972
* Added general dbxref UM-BBD_enzymeID:e0417 to GO:0019164
* Added general dbxref UM-BBD_enzymeID:e0674 to GO:0019874
* Added general dbxref UM-BBD_enzymeID:e0673 to GO:0019875
* Added general dbxref UM-BBD_enzymeID:e0515 to GO:0030791
* Copied GO:0032774 to GO:0044249 with type OBO_REL:is_a
* Added general dbxref UM-BBD_enzymeID:e0650 to GO:0033734
* Added general dbxref UM-BBD_enzymeID:e0479 to GO:0033767
* Added general dbxref UM-BBD_enzymeID:e0508 to GO:0033797
* Deleted GO:0033863 --OBO_REL:is_a--> GO:0016301
* Copied GO:0033863 to GO:0019200 with type OBO_REL:is_a
* Added general dbxref UM-BBD_enzymeID:e0953 to GO:0034022
* Added synonym "arthropod blood cell migration" to GO:0035099
* Changed synonym scope of GO:0035099 from "Related" to "Exact"
* Added synonym "embryonic arthropod blood cell differentiation" to GO:0035163
* Changed synonym scope of GO:0035163 from "Related" to "Exact"
* Added synonym "larval lymph gland arthropod blood cell differentiation" to GO:0035168
* Changed synonym scope of GO:0035168 from "Related" to "Exact"
* Added synonym "arthropod blood cell proliferation" to GO:0035172
* Changed synonym scope of GO:0035172 from "Related" to "Exact"
* Added synonym "regulation of arthropod blood cell proliferation" to GO:0035206
* Changed synonym scope of GO:0035206 from "Related" to "Exact"
* Added synonym "negative regulation of arthropod blood cell proliferation" to GO:0035207
* Changed synonym scope of GO:0035207 from "Related" to "Exact"
* Added synonym "positive regulation of arthropod blood cell proliferation" to GO:0035208
* Changed synonym scope of GO:0035208 from "Related" to "Exact"
* Added synonym "arthropod blood cell differentiation" to GO:0042386
* Changed synonym scope of GO:0042386 from "Related" to "Exact"
* Added synonym "regulation of arthropod blood cell differentiation" to GO:0045610
* Changed synonym scope of GO:0045610 from "Related" to "Exact"
* Added synonym "negative regulation of arthropod blood cell differentiation" to GO:0045611
* Changed synonym scope of GO:0045611 from "Related" to "Exact"
* Added synonym "positive regulation of arthropod blood cell differentiation" to GO:0045612
* Changed synonym scope of GO:0045612 from "Related" to "Exact"
* Added general dbxref UM-BBD_enzymeID:e0715 to GO:0047071
* Added general dbxref UM-BBD_enzymeID:e0889 to GO:0047073
* Added general dbxref UM-BBD_enzymeID:e0911 to GO:0047075
* Added general dbxref UM-BBD_enzymeID:e0904 to GO:0047102
* Added general dbxref UM-BBD_enzymeID:e0853 to GO:0047104
* Added general dbxref UM-BBD_enzymeID:e0855 to GO:0047133
* Added general dbxref UM-BBD_enzymeID:e0609 to GO:0047143
* Added general dbxref UM-BBD_enzymeID:e0576 to GO:0047154
* Added general dbxref UM-BBD_enzymeID:e0905 to GO:0047437
* Added general dbxref UM-BBD_enzymeID:e0896 to GO:0047544
* Added general dbxref UM-BBD_enzymeID:e0951 to GO:0047549
* Added general dbxref UM-BBD_enzymeID:e0654 to GO:0047569
* Added general dbxref UM-BBD_enzymeID:e0868 to GO:0047621
* Added general dbxref UM-BBD_enzymeID:e0481 to GO:0047806
* Added general dbxref UM-BBD_enzymeID:e0734 to GO:0047924
* Added general dbxref UM-BBD_enzymeID:e0721 to GO:0047925
* Added general dbxref UM-BBD_enzymeID:e0722 to GO:0050005
* Added general dbxref UM-BBD_enzymeID:e0874 to GO:0050061
* Deleted GO:0050148 --OBO_REL:is_a--> GO:0016301
* Added general dbxref UM-BBD_enzymeID:e0875 to GO:0050352
* Added general dbxref UM-BBD_enzymeID:e0551 to GO:0050381
* Added general dbxref UM-BBD_enzymeID:e0655 to GO:0050390
* Added general dbxref UM-BBD_enzymeID:e0514 to GO:0050446
* Added general dbxref UM-BBD_enzymeID:e0854 to GO:0050470
* Added general dbxref UM-BBD_enzymeID:e0638 to GO:0050549
* Added general dbxref UM-BBD_enzymeID:e0538 to GO:0050555
* Added general dbxref UM-BBD_enzymeID:e0539 to GO:0050574
* Added general dbxref UM-BBD_enzymeID:e0540 to GO:0050575
* Added general dbxref UM-BBD_enzymeID:e0610 to GO:0050587
* Added general dbxref UM-BBD_enzymeID:e0775 to GO:0050603
* Added general dbxref UM-BBD_enzymeID:e0658 to GO:0050609
* Added general dbxref UM-BBD_enzymeID:e0528 to GO:0050610
* Added general dbxref UM-BBD_enzymeID:e0541 to GO:0050628
* Added general dbxref UM-BBD_enzymeID:e0652 to GO:0050695
* Added general dbxref UM-BBD_enzymeID:e0710 to GO:0051907

From gocvs at genome.stanford.edu  Wed Jun 18 21:30:49 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Wed, 18 Jun 2008 21:30:49 -0700 (PDT)
Subject: [Go-diff] GO update 06/18/2008
Message-ID: <200806190430.VAA24363@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.112 by 1.113

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Added synonym "negative regulation of host intracellular antiviral response by virus" to GO:0019052
* Changed synonym scope of GO:0019052 from "Related" to "Exact"
* Added synonym "suppression of host intracellular antiviral response by virus" to GO:0019052
* Changed synonym scope of GO:0019052 from "Related" to "Exact"
* Added synonym "negative regulation of host extracellular antiviral response by virus" to GO:0019053
* Changed synonym scope of GO:0019053 from "Related" to "Exact"
* Added synonym "suppression of host extracellular antiviral response by virus" to GO:0019053
* Changed synonym scope of GO:0019053 from "Related" to "Exact"
* Added synonym "modulation by virus of host cellular process" to GO:0019054
* Changed synonym scope of GO:0019054 from "Related" to "Exact"
* Added synonym "modulation of cellular process in host by virus" to GO:0019054
* Added synonym "regulation by virus of host cellular process" to GO:0019054
* Changed synonym scope of GO:0019054 from "Related" to "Exact"
* Added synonym "regulation of cellular process in host by virus" to GO:0019054
* Changed synonym scope of GO:0019054 from "Related" to "Exact"
* Added synonym "regulation of host cellular process by virus" to GO:0019054
* Changed synonym scope of GO:0019054 from "Related" to "Exact"
* Changed name of GO:0019057 from "regulation of host cell mRNA translation by virus" to "regulation of host mRNA translation by virus"
* Added synonym "regulation of host translation by virus" to GO:0019057
* Changed synonym scope of GO:0019057 from "Related" to "Exact"
* Added synonym "regulation of translation in host by virus" to GO:0019057
* Changed synonym scope of GO:0019057 from "Related" to "Exact"
* Added synonym "modification of catalytic activity of host by symbiont" to GO:0052148
* Changed synonym scope of GO:0052148 from "Related" to "Exact"
* Added synonym "regulation by symbiont of host catalytic activity" to GO:0052148
* Changed synonym scope of GO:0052148 from "Related" to "Exact"
* Added synonym "regulation of catalytic activity of host by symbiont" to GO:0052148
* Changed synonym scope of GO:0052148 from "Related" to "Exact"
* Added synonym "regulation of host catalytic activity by symbiont" to GO:0052148
* Changed synonym scope of GO:0052148 from "Related" to "Exact"

From gocvs at genome.stanford.edu  Mon Jun 23 21:30:47 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Mon, 23 Jun 2008 21:30:47 -0700 (PDT)
Subject: [Go-diff] GO update 06/23/2008
Message-ID: <200806240430.VAA05412@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.113 by 1.115

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010623
* Populated new object GO:0010623 (macro)
  * Changed name of GO:0010623 from "<new term>" to "developmental programmed cell death"
  * Set definition of GO:0010623 to "The activation of endogenous cellular processes that result in the death of a cell as part of its development."
  * Added definition dbxref GOC:dph to GO:0010623
  * Added definition dbxref GOC:tb to GO:0010623
  * Copied GO:0010623 to GO:0048468 with type part_of
  * Copied GO:0010623 to GO:0012501 with type OBO_REL:is_a
  * Copied GO:0010623 to GO:0048869 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010623
* Added synonym "Rhp51-dependent recombinational repair" to GO:0000724
* Changed synonym scope of GO:0000724 from "Related" to "Narrow"
* Added synonym "bone development" to GO:0001501
* Added general dbxref GOC:tb to synonym bone development of GO:0001501
* Added general dbxref GOC:dph to synonym bone development of GO:0001501
* Changed synonym scope of GO:0001501 from "Related" to "Narrow"
* Changed definition of GO:0001941 from "The maintenance of membrane compostition in a postsynaptic membrane, the specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft)." to "The maintenance of membrane composition in a postsynaptic membrane, the specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft)."
* Changed synonym scope of GO:0004152 from "Exact" to "Narrow"
* Added synonym "(DHO) dehydrogenase activity" to GO:0004152
* Added general dbxref EC:1.3.3.1 to synonym (DHO) dehydrogenase activity of GO:0004152
* Added synonym "DHOdehase activity" to GO:0004152
* Added general dbxref EC:1.3.3.1 to synonym DHOdehase activity of GO:0004152
* Changed synonym scope of GO:0004152 from "Related" to "Exact"
* Added synonym "dihydoorotic acid dehydrogenase activity" to GO:0004152
* Added general dbxref EC:1.3.3.1 to synonym dihydoorotic acid dehydrogenase activity of GO:0004152
* Changed synonym scope of GO:0004152 from "Related" to "Exact"
* Deleted synonym "(DHO) dehydrogenase activity" from GO:0004158
* Deleted synonym "DHOdehase activity" from GO:0004158
* Deleted synonym "dihydoorotic acid dehydrogenase activity" from GO:0004158
* Copied GO:0004158 to GO:0004152 with type OBO_REL:is_a
* Copied GO:0005451 to GO:0015299 with type OBO_REL:is_a
* Deleted GO:0008219 --OBO_REL:is_a--> GO:0048869
* Deleted GO:0008219 --part_of--> GO:0048468
* Copied GO:0008219 to GO:0009987 with type OBO_REL:is_a
* Deleted GO:0010198 --OBO_REL:is_a--> GO:0012501
* Copied GO:0010198 to GO:0010623 with type OBO_REL:is_a
* Deleted GO:0017059 --OBO_REL:is_a--> GO:0044432
* Deleted GO:0017059 --OBO_REL:is_a--> GO:0044425
* Deleted GO:0017059 --part_of--> GO:0005789
* Deleted GO:0031017 --OBO_REL:is_a--> GO:0031016
* Copied GO:0031017 to GO:0048856 with type OBO_REL:is_a
* Copied GO:0031017 to GO:0031016 with type part_of
* Deleted GO:0031018 --OBO_REL:is_a--> GO:0031016
* Copied GO:0031018 to GO:0031016 with type part_of
* Copied GO:0031018 to GO:0048856 with type OBO_REL:is_a
* Changed definition of GO:0032502 from "A biological process whose specific outcome is the progression of an integrated living unit: a cell, tissue, organ, or organism over time from an initial condition to a later condition." to "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition."
* Deleted GO:0035096 --OBO_REL:is_a--> GO:0012501
* Copied GO:0035096 to GO:0010623 with type OBO_REL:is_a
* Deleted GO:0035234 --OBO_REL:is_a--> GO:0012501
* Copied GO:0035234 to GO:0010623 with type OBO_REL:is_a
* Changed name of GO:0042132 from "fructose-bisphosphatase activity" to "fructose 1,6-bisphosphate 1-phosphatase activity"
* Deleted synonym "fructose 1,6-bisphosphate 1-phosphatase activity" from GO:0042132
* Added synonym "fructose-bisphosphatase activity" to GO:0042132
* Added general dbxref EC:3.1.3.00 to synonym fructose-bisphosphatase activity of GO:0042132
* Changed synonym scope of GO:0042132 from "Related" to "Broad"
* Deleted GO:0043769 --part_of--> GO:0000781
* Deleted GO:0046666 --OBO_REL:is_a--> GO:0012501
* Copied GO:0046666 to GO:0010623 with type OBO_REL:is_a
* Deleted GO:0055045 --OBO_REL:is_a--> GO:0012501
* Copied GO:0055045 to GO:0010623 with type OBO_REL:is_a
* Deleted GO:0055118 --OBO_REL:is_a--> GO:0045932

From gocvs at genome.stanford.edu  Tue Jun 24 21:30:47 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Tue, 24 Jun 2008 21:30:47 -0700 (PDT)
Subject: [Go-diff] GO update 06/24/2008
Message-ID: <200806250430.VAA26674@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.115 by 1.116

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034515
* Populated new object GO:0034515 (macro)
  * Changed name of GO:0034515 from "<new term>" to "proteasome storage granule"
  * Set definition of GO:0034515 to "A multisubunit proteasome complex that localizes in
the cytoplasm as dot-like structures when cells are in a quiescent state."
  * Added definition dbxref GOC:rb to GO:0034515
  * Added definition dbxref PMID:18504300 to GO:0034515
  * Added synonym "PSG" to GO:0034515
  * Changed synonym scope of GO:0034515 from "Related" to "Exact"
  * Copied GO:0034515 to GO:0031597 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034515
* Changed definition of GO:0005746 from "The protein complexes that form the mitochondrial electron transport system (the respiratory chain). Complexes I, III and IV can transport protons if embedded in an oriented membrane, such as an intact mitochondrial inner membrane." to "The protein complexes that form the mitochondrial electron transport system (the respiratory chain), associated with the inner mitochondrial membrane. Complexes I, III and IV can transport protons if embedded in an oriented membrane, such as an intact mitochondrial inner membrane."
* Added definition dbxref GOC:curators to GO:0005746
* Changed definition of GO:0005747 from "A part of the respiratory chain located in the mitochondrion. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone." to "A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone."
* Changed definition of GO:0005749 from "A part of the respiratory chain located in the mitochondrion, containing the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain." to "A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain."
* Changed definition of GO:0005750 from "A part of the respiratory chain located in the mitochondrion, containing about 10 polypeptide subunits including four redox centers: cytochrome b/b6, cytochrome c1 and an 2Fe-2S cluster. Catalyzes the oxidation of ubiquinol by oxidized cytochrome c1." to "A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains about 10 polypeptide subunits including four redox centers: cytochrome b/b6, cytochrome c1 and an 2Fe-2S cluster. Catalyzes the oxidation of ubiquinol by oxidized cytochrome c1."
* Changed definition of GO:0005751 from "A part of the respiratory chain located in the mitochondrion, containing the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2). Found in eukaryotes." to "A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2)."
* Changed definition of GO:0034464 from "A protein complex that associates with the primary cilium and is cilium biogenesis; consists of seven conserved proteins: BBS1, BBS2, BBS4, BBS5, BBS7, BBS8 and BBS9." to "A protein complex that associates with the primary cilium and is involved in cilium biogenesis; consists of seven conserved proteins: BBS1, BBS2, BBS4, BBS5, BBS7, BBS8 and BBS9."

From gocvs at genome.stanford.edu  Thu Jun 26 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Thu, 26 Jun 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 06/26/2008
Message-ID: <200806270430.VAA19089@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.116 by 1.118

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034516
* Created object of type obo:TERM with id GO:0034517
* Created object of type obo:TERM with id GO:0034520
* Created object of type obo:TERM with id GO:0034521
* Created object of type obo:TERM with id GO:0034522
* Created object of type obo:TERM with id GO:0034523
* Created object of type obo:TERM with id GO:0034524
* Created object of type obo:TERM with id GO:0034525
* Created object of type obo:TERM with id GO:0034526
* Created object of type obo:TERM with id GO:0034527
* Created object of type obo:TERM with id GO:0034528
* Created object of type obo:TERM with id GO:0034529
* Created object of type obo:TERM with id GO:0034530
* Created object of type obo:TERM with id GO:0034531
* Created object of type obo:TERM with id GO:0034532
* Created object of type obo:TERM with id GO:0034533
* Created object of type obo:TERM with id GO:0034534
* Crea