From gocvs at genome.stanford.edu Wed Apr 2 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Wed, 2 Apr 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 04/02/2008 Message-ID: <200804030430.VAA11036@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.748 by 5.749 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Copied GO:0000179 to GO:0008170 with type OBO_REL:is_a * Removed GO:0000289 from category gosubset_prok * Deleted GO:0000289 --OBO_REL:is_a--> GO:0031124 * Copied GO:0000289 to GO:0006402 with type OBO_REL:is_a * Copied GO:0000335 to GO:0045910 with type OBO_REL:is_a * Copied GO:0000336 to GO:0045911 with type OBO_REL:is_a * Copied GO:0002652 to GO:0002819 with type OBO_REL:is_a * Deleted synonym "caldesmon kinase activity" from GO:0004683 * Deleted synonym "Wnt receptor activity" from GO:0004928 * Deleted synonym "Wnt receptor activity" from GO:0004929 * Deleted synonym "secretory granule" from GO:0005803 * Deleted synonym "transport vesicle" from GO:0005803 * Deleted synonym "mating projection" from GO:0005936 * Deleted GO:0006313 --OBO_REL:is_a--> GO:0006310 * Copied GO:0007096 to GO:0010564 with type OBO_REL:is_a * Deleted synonym "positive regulation of JNK activity" from GO:0007257 * Deleted synonym "positive regulation of JUNK activity" from GO:0007257 * Deleted GO:0007587 --OBO_REL:is_a--> GO:0005975 * Copied GO:0007587 to GO:0007586 with type OBO_REL:is_a * Deleted GO:0007611 --OBO_REL:is_a--> GO:0032501 * Deleted GO:0007632 --OBO_REL:is_a--> GO:0032501 * Copied GO:0008988 to GO:0008170 with type OBO_REL:is_a * Copied GO:0008989 to GO:0008170 with type OBO_REL:is_a * Copied GO:0008990 to GO:0008170 with type OBO_REL:is_a * Deleted synonym "capsule" from GO:0009278 * Copied GO:0009383 to GO:0008169 with type OBO_REL:is_a * Deleted GO:0010467 --OBO_REL:is_a--> GO:0009987 * Copied GO:0010467 to GO:0008150 with type OBO_REL:is_a * Deleted GO:0010468 --OBO_REL:is_a--> GO:0050794 * Copied GO:0010468 to GO:0050789 with type OBO_REL:is_a * Copied GO:0010503 to GO:0032108 with type OBO_REL:is_a * Copied GO:0010520 to GO:0010564 with type OBO_REL:is_a * Copied GO:0010535 to GO:0050731 with type OBO_REL:is_a * Deleted GO:0015385 --OBO_REL:is_a--> GO:0015299 * Deleted definition dbxref PMID:17511809 from GO:0015616 * Copied GO:0019607 to GO:0042135 with type OBO_REL:is_a * Copied GO:0019787 to GO:0003824 with type OBO_REL:is_a * Deleted GO:0022900 --OBO_REL:is_a--> GO:0055114 * Copied GO:0030071 to GO:0010564 with type OBO_REL:is_a * Deleted definition dbxref GOC:dph from GO:0030534 * Deleted definition dbxref GOC:tb from GO:0030534 * Copied GO:0030743 to GO:0008171 with type OBO_REL:is_a * Deleted GO:0032196 --OBO_REL:is_a--> GO:0009987 * Copied GO:0032196 to GO:0006310 with type OBO_REL:is_a * Copied GO:0032430 to GO:0060193 with type OBO_REL:is_a * Copied GO:0032884 to GO:0051128 with type OBO_REL:is_a * Deleted synonym "1,5-anhydro-D-fructose reductase activity" from GO:0033712 * Deleted synonym "aldehyde oxidase activity" from GO:0033727 * Deleted synonym "glucoside 3-dehydrogenase" from GO:0033757 * Deleted synonym "6G-fructosyltransferase activity" from GO:0033841 * Deleted synonym "thiol sulfotransferase activity" from GO:0033870 * Deleted synonym "scymnol sulfotransferase activity" from GO:0033874 * Deleted synonym "ribonuclease T2 activity" from GO:0033897 * Deleted synonym "RNase U2 activity" from GO:0033899 * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Deleted GO:0033932 --OBO_REL:is_a--> GO:0004553 * Copied GO:0033932 to GO:0004560 with type OBO_REL:is_a * Deleted synonym "alpha-L-fucosidase activity" from GO:0033938 * Deleted GO:0033938 --OBO_REL:is_a--> GO:0004553 * Copied GO:0033938 to GO:0004560 with type OBO_REL:is_a * Deleted synonym "inulinase activity" from GO:0033948 * Deleted synonym "2-haloacid dehalogenase (configuration-inverting) activity" from GO:0033976 * Deleted synonym "2-haloacid dehalogenase (configuration-retaining) activity" from GO:0033977 * Deleted synonym "glucuronan lyase activity" from GO:0033994 * Deleted synonym "chondroitin B lyase activity" from GO:0033999 * Deleted synonym "chondroitin ABC lyase activity" from GO:0034000 * Deleted synonym "chondroitin-sulfate-ABC endolyase activity" from GO:0034000 * Deleted GO:0034000 --OBO_REL:is_a--> GO:0016837 * Copied GO:0034000 to GO:0047486 with type OBO_REL:is_a * Deleted synonym "chondroitin ABC lyase activity" from GO:0034001 * Deleted synonym "chondroitin-sulfate-ABC exolyase activity" from GO:0034001 * Deleted GO:0034001 --OBO_REL:is_a--> GO:0016837 * Copied GO:0034001 to GO:0047486 with type OBO_REL:is_a * Deleted synonym "L-ribulose-5-phosphate 3-epimerase activity" from GO:0034015 * Deleted synonym "DNA polymerase activity" from GO:0034061 * Copied GO:0034091 to GO:0010564 with type OBO_REL:is_a * Deleted GO:0035187 --OBO_REL:is_a--> GO:0032501 * Deleted synonym "inositol-1,3,4-trisphosphate 5/6-kinase activity" from GO:0035300 * Deleted synonym "host cell nucleus" from GO:0042025 * Copied GO:0042443 to GO:0042133 with type OBO_REL:is_a * Copied GO:0042444 to GO:0042136 with type OBO_REL:is_a * Deleted synonym "vitamin B6 metabolic process" from GO:0042817 * Deleted synonym "vitamin B6 metabolism" from GO:0042817 * Copied GO:0043286 to GO:0009889 with type OBO_REL:is_a * Deleted synonym "regulation of MAP kinase activity" from GO:0043405 * Deleted synonym "positive regulation of MAP kinase activity" from GO:0043406 * Deleted synonym "negative regulation of MAP kinase activity" from GO:0043407 * Deleted synonym "methylamine-specific methylcobalamin:coenzyme M methyltransferase activity" from GO:0043833 * Deleted synonym "protein stabilization" from GO:0045185 * Copied GO:0045212 to GO:0009059 with type OBO_REL:is_a * Deleted synonym "9-cis-epoxycarotenoid dioxygenase activity" from GO:0045549 * Deleted synonym "positive regulation of translation" from GO:0045727 * Copied GO:0045798 to GO:0051053 with type OBO_REL:is_a * Copied GO:0045799 to GO:0051054 with type OBO_REL:is_a * Deleted synonym "negative regulation of mitotic cell cycle" from GO:0045930 * Deleted synonym "positive regulation of mitotic cell cycle" from GO:0045931 * Copied GO:0045936 to GO:0031324 with type OBO_REL:is_a * Copied GO:0045937 to GO:0031325 with type OBO_REL:is_a * Deleted synonym "positive regulation of mitotic cell cycle, embryonic" from GO:0045977 * Copied GO:0046017 to GO:0022402 with type OBO_REL:is_a * Copied GO:0046020 to GO:0000122 with type OBO_REL:is_a * Copied GO:0046021 to GO:0022402 with type OBO_REL:is_a * Copied GO:0046023 to GO:0022402 with type OBO_REL:is_a * Deleted synonym "ATP-dependent polynucleotide kinase activity" from GO:0046404 * Deleted synonym "violaxanthin de-epoxidase activity" from GO:0046422 * Copied GO:0046599 to GO:0010564 with type OBO_REL:is_a * Deleted synonym "1-acylglycerophosphocholine O-acyltransferase activity" from GO:0047184 * Deleted synonym "galactinol-raffinose galactosyltransferase activity" from GO:0047268 * Deleted GO:0047513 --OBO_REL:is_a--> GO:0004553 * Copied GO:0047513 to GO:0004560 with type OBO_REL:is_a * Deleted synonym "2,3-dihydroxyindole 2,3-dioxygenase activity" from GO:0047528 * Deleted synonym "CDP-abequose epimerase activity" from GO:0047732 * Deleted synonym "[citrate-(pro-3S)-lyase] thiolesterase activity" from GO:0047778 * Deleted synonym "cyclohexadienyl dehydrogenase activity" from GO:0047794 * Deleted synonym "erythrose-4-phosphate dehydrogenase activity" from GO:0048001 * Deleted GO:0048266 --OBO_REL:is_a--> GO:0032501 * Deleted synonym "L-galactonolactone oxidase activity" from GO:0050024 * Deleted synonym "lathosterol oxidase activity" from GO:0050046 * Deleted synonym "prostaglandin-E2 9-reductase activity" from GO:0050221 * Deleted synonym "rhodopsin kinase activity" from GO:0050254 * Deleted synonym "deoxyhypusine synthase activity" from GO:0050983 * Deleted synonym "positive regulation of NK T cell activation" from GO:0051135 * Deleted synonym "regulation of NK T cell proliferation" from GO:0051140 * Deleted synonym "regulation of ubiquitin-protein ligase activity" from GO:0051438 * Deleted synonym "regulation of meiotic cell cycle" from GO:0051445 * Deleted synonym "GTP-dependent polynucleotide kinase activity" from GO:0051735 * Deleted synonym "UTP-monosaccharide-1-phosphate uridylyltransferase activity" from GO:0051748 * Deleted synonym "phosphoglucan, water dikinase activity" from GO:0051752 * Deleted synonym "positive regulation by symbiont of host apoptosis" from GO:0052151 * Deleted GO:0055114 --OBO_REL:is_a--> GO:0008152 * Deleted GO:0022900 --OBO_REL:is_a--> GO:0055114 * Destroyed object GO:0055114 From gocvs at genome.stanford.edu Thu Apr 3 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Thu, 3 Apr 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 04/03/2008 Message-ID: <200804040430.VAA25677@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.749 by 5.750 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034357 * Created object of type obo:TERM with id GO:0055114 * Populated new object GO:0034357 (macro) * Changed name of GO:0034357 from "" to "photosynthetic membrane" * Set definition of GO:0034357 to "A membrane enriched in complexes formed of reaction centers, accessory pigments and electron carriers, in which photosynthetic reactions take place." * Added definition dbxref GOC:ds to GO:0034357 * Added definition dbxref GOC:mah to GO:0034357 * Copied GO:0034357 to GO:0016020 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034357 * Populated new object GO:0055114 (macro) * Changed name of GO:0055114 from "" to "oxidation reduction" * Set definition of GO:0055114 to "The process of removal or addition of one or more electrons with or without the concomitant removal or addition of a proton or protons." * Added definition dbxref GOC:dl to GO:0055114 * Added definition dbxref GOC:ed to GO:0055114 * Added definition dbxref GOC:jid to GO:0055114 * Added definition dbxref GOC:jm to GO:0055114 * Added definition dbxref GOC:mlg to GO:0055114 * Added definition dbxref GOC:rh to GO:0055114 * Added synonym "electron transport process" to GO:0055114 * org.geneontology.oboedit.datamodel.history.ChangeSynCategoryHistoryItem at f81c84 * Changed synonym scope of GO:0055114 from "Related" to "Exact" * Added synonym "oxidoreductase process" to GO:0055114 * org.geneontology.oboedit.datamodel.history.ChangeSynCategoryHistoryItem at 1185f3b * Changed synonym scope of GO:0055114 from "Related" to "Exact" * Copied GO:0055114 to GO:0008152 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0055114 * Changed name of GO:0001410 from "chlamydospore development" to "chlamydospore formation" * Changed definition of GO:0001410 from "The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. Chlamydospores are thick-walled, spore-like cells borne on the ends of elongated cells attached to hyphae or pseudohyphae, seen in the species Candida albicans and Candida dubliniensis. Note that although these structures resemble the chlamydospores of other fungi, it is not known whether they are true spores, so this process is not currently considered a type of spore formation." to "The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. A chlamydospores is a mitotic (asexual) one-celled spore, produced primarily for survival, not dispersal, originating endogenously and singly within part of a pre-existing cell and possessing an inner secondary and often thickened cell wall." * Added definition dbxref ISBN:085199377X to GO:0001410 * Changed synonym scope of GO:0001410 from "Related" to "Narrow" * Deleted synonym "chlamydospore formation" from GO:0001410 * Added synonym "chlamydospore development" to GO:0001410 * Changed synonym scope of GO:0001410 from "Related" to "Exact" * Copied GO:0001410 to GO:0030436 with type OBO_REL:is_a * added secondary id GO:0030090 to GO:0009521 * Changed definition of GO:0009521 from "One of the photochemical systems containing photosynthetic and accessory pigments and electron carriers that operate in sequence to perform the two light reactions of photosynthesis." to "A complex located in a photosynthetic membrane that consists of a photoreaction center associated with accessory pigments and electron carriers." * Added definition dbxref GOC:ds to GO:0009521 * Added definition dbxref GOC:mah to GO:0009521 * Added definition dbxref PMID:9821949 to GO:0009521 * Added synonym "reaction center (sensu Gram-negative Bacteria)" to GO:0009521 * Changed synonym scope of GO:0009521 from "Related" to "Narrow" * Added synonym "reaction center (sensu Proteobacteria)" to GO:0009521 * Changed synonym scope of GO:0009521 from "Related" to "Narrow" * Added synonym "reaction centre (sensu Gram-negative Bacteria)" to GO:0009521 * Changed synonym scope of GO:0009521 from "Related" to "Narrow" * Added synonym "reaction centre (sensu Proteobacteria)" to GO:0009521 * Changed synonym scope of GO:0009521 from "Related" to "Narrow" * Deleted GO:0009521 --OBO_REL:is_a--> GO:0044436 * Copied GO:0009521 to GO:0034357 with type part_of * Changed definition of GO:0009522 from "Photosystem that functions as a light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin to ferredoxin." to "A photosystem that contains an iron-sulfur reaction center associated with accessory pigments and electron carriers. In cyanobacteria and chloroplasts, photosystem I functions as a light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin to ferredoxin; in photosynthetic bacteria that have only a single type I photosystem, such as the green sulfur bacteria, electrons can go either to ferredoxin (Fd) -> NAD+ or to menaquinone (MK) -> Cytb/FeS -> Cytc555 -> photosystem I (cyclic photophosphorylation)." * Deleted definition dbxref ISBN:0943088399 from GO:0009522 * Added definition dbxref GOC:ds to GO:0009522 * Added definition dbxref GOC:mah to GO:0009522 * Added definition dbxref ISBN:0140514031 to GO:0009522 * Added definition dbxref PMID:9821949 to GO:0009522 * Changed definition of GO:0009523 from "An integral membrane complex containing the P680 reaction center. In the light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone." to "A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers. In cyanobacteria and chloroplasts, in the presence of light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone, whereas other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center." * Added definition dbxref GOC:ds to GO:0009523 * Added definition dbxref GOC:mah to GO:0009523 * Added definition dbxref PMID:9821949 to GO:0009523 * Deleted GO:0009538 --OBO_REL:is_a--> GO:0044436 * Deleted GO:0009539 --OBO_REL:is_a--> GO:0044436 * Changed definition of GO:0009579 from "A membraneous cellular structure that bears the photosynthetic pigments in photosynthetic organisms. In prokaryotes the thylakoids are of various shapes and are attached to the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." to "A membraneous cellular structure that bears the photosynthetic pigments in photosynthetic organisms. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." * Added definition dbxref GOC:ds to GO:0009579 * Deleted GO:0009579 --OBO_REL:is_a--> GO:0043231 * Copied GO:0009579 to GO:0034357 with type OBO_REL:is_a * Deleted GO:0009782 --OBO_REL:is_a--> GO:0044436 * Deleted GO:0009783 --OBO_REL:is_a--> GO:0044436 * Deleted GO:0009941 --OBO_REL:is_a--> GO:0016020 * Copied GO:0022900 to GO:0055114 with type OBO_REL:is_a * Deleted GO:0030090 --OBO_REL:is_a--> GO:0009521 * Destroyed object GO:0030090 * Copied GO:0030093 to GO:0044436 with type OBO_REL:is_a * Copied GO:0030095 to GO:0044436 with type OBO_REL:is_a * Copied GO:0031976 to GO:0043231 with type OBO_REL:is_a * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Changed name of GO:0034299 from "blastospore formation" to "reproductive blastospore formation" * Added comment "Note that this term should not be confused with the usage of 'blastospore' to mean any yeast-form fungal cell, as in Candida species." * Changed definition of GO:0034299 from "The formation of produced from a vegetative mother cell by budding. Blastospores are a type of asexual spore found in some fungi, including Candida species and the class Glomeromycota." to "The formation of a spore following the marked enlargement of part of a cell before separation by a septum. Blastospores are a type of asexual spore found in some fungi, most notably the class Glomeromycota." * Deleted definition dbxref GOC:ds from GO:0034299 * Deleted definition dbxref ISBN:?? from GO:0034299 * Added definition dbxref GOC:mah to GO:0034299 * Added definition dbxref http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_a_b.shtml#blastospore to GO:0034299 * Added definition dbxref http://bugs.bio.usyd.edu.au/Mycology/Taxonomy/glomeromycota.shtml to GO:0034299 * Copied GO:0042649 to GO:0043231 with type OBO_REL:is_a From gocvs at genome.stanford.edu Fri Apr 4 21:30:46 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Fri, 4 Apr 2008 21:30:46 -0700 (PDT) Subject: [Go-diff] GO update 04/04/2008 Message-ID: <200804050430.VAA05916@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.750 by 5.751 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0060231 * Populated new object GO:0060231 (macro) * Changed name of GO:0060231 from "" to "mesenchymal to epithelial transition" * Set definition of GO:0060231 to "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell." * Added definition dbxref GOC:dph to GO:0060231 * Added synonym "mesenchymal-epithelial transition" to GO:0060231 * Added general dbxref GOC:dph to synonym mesenchymal-epithelial transition of GO:0060231 * Changed synonym scope of GO:0060231 from "Related" to "Exact" * Copied GO:0060231 to GO:0002064 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0060231 * Changed definition of GO:0003008 from "A biological process, occurring at the level of an organ system pertinent to the function of the organism. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." to "A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective." * Changed definition of GO:0003013 from "The biological processes, occurring at the level of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." to "A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." * Changed definition of GO:0003014 from "The biological processes, occurring at the level of the renal system. The renal system is responsible for fluid volume regulation and detoxification in an organism." to "A organ system process carried out by any of the organs or tissues of the renal system. The renal system is responsible for fluid volume regulation and detoxification in an organism." * Changed definition of GO:0003015 from "The biological processes, occurring at the level of the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." to "A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." * Changed definition of GO:0003016 from "The biological processes, occurring at the level of the resiratory system. The respiratory system is an organ system responsible for respiratory gasseous exchange." to "A organ system process carried out by any of the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gasseous exchange." * Copied GO:0007611 to GO:0032501 with type OBO_REL:is_a * Copied GO:0007632 to GO:0032501 with type OBO_REL:is_a * Deleted GO:0010467 --OBO_REL:is_a--> GO:0008150 * Copied GO:0010467 to GO:0009987 with type OBO_REL:is_a * Deleted GO:0010468 --OBO_REL:is_a--> GO:0050789 * Copied GO:0010468 to GO:0050794 with type OBO_REL:is_a * Changed name of GO:0010531 from "activation of JAK1 protein" to "activation of JAK1 kinase activity" * Added synonym "activation of JAK1 protein" to GO:0010531 * Added general dbxref GOC:tb to synonym activation of JAK1 protein of GO:0010531 * Added general dbxref GOC:dph to synonym activation of JAK1 protein of GO:0010531 * Changed synonym scope of GO:0010531 from "Related" to "Exact" * Changed name of GO:0010532 from "regulation of activation of JAK1 protein" to "regulation of activation of JAK1 kinase activity" * Added synonym "regulation of activation of JAK1 protein" to GO:0010532 * Added general dbxref GOC:tb to synonym regulation of activation of JAK1 protein of GO:0010532 * Added general dbxref GOC:dph to synonym regulation of activation of JAK1 protein of GO:0010532 * Changed synonym scope of GO:0010532 from "Related" to "Exact" * Changed name of GO:0010533 from "regulation of activation of JAK protein" to "regulation of activation of Janus kinase activity" * Added synonym "regulation of activation of JAK protein" to GO:0010533 * Added general dbxref GOC:tb to synonym regulation of activation of JAK protein of GO:0010533 * Added general dbxref GOC:dph to synonym regulation of activation of JAK protein of GO:0010533 * Changed synonym scope of GO:0010533 from "Related" to "Exact" * Changed name of GO:0010534 from "regulation of activation of JAK2 protein" to "regulation of activation of JAK2 kinase activity" * Added synonym "regulation of activation of JAK2 protein" to GO:0010534 * Added general dbxref GOC:tb to synonym regulation of activation of JAK2 protein of GO:0010534 * Added general dbxref GOC:dph to synonym regulation of activation of JAK2 protein of GO:0010534 * Changed synonym scope of GO:0010534 from "Related" to "Exact" * Changed name of GO:0010535 from "positive regulation of activation of JAK2 protein" to "positive regulation of activation of JAK2 kinase activity" * Added synonym "positive regulation of activation of JAK2 protein" to GO:0010535 * Added general dbxref GOC:tb to synonym positive regulation of activation of JAK2 protein of GO:0010535 * Added general dbxref GOC:dph to synonym positive regulation of activation of JAK2 protein of GO:0010535 * Changed synonym scope of GO:0010535 from "Related" to "Exact" * Deleted GO:0010535 --OBO_REL:is_a--> GO:0050731 * Changed name of GO:0010536 from "positive regulation of activation of JAK protein" to "positive regulation of activation of Janus kinase activity" * Added synonym "positive regulation of activation of JAK protein" to GO:0010536 * Added general dbxref GOC:tb to synonym positive regulation of activation of JAK protein of GO:0010536 * Added general dbxref GOC:dph to synonym positive regulation of activation of JAK protein of GO:0010536 * Changed synonym scope of GO:0010536 from "Related" to "Exact" * Changed name of GO:0010537 from "positive regulation of activation of JAK1 protein" to "positive regulation of activation of JAK1 kinase activity" * Added synonym "positive regulation of activation of JAK1 protein" to GO:0010537 * Added general dbxref GOC:tb to synonym positive regulation of activation of JAK1 protein of GO:0010537 * Added general dbxref GOC:dph to synonym positive regulation of activation of JAK1 protein of GO:0010537 * Changed synonym scope of GO:0010537 from "Related" to "Exact" * Copied GO:0030534 to GO:0032501 with type OBO_REL:is_a * Copied GO:0030537 to GO:0032501 with type OBO_REL:is_a * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Copied GO:0035187 to GO:0032501 with type OBO_REL:is_a * Changed name of GO:0042976 from "activation of JAK protein" to "activation of Janus kinase activity" * Added synonym "activation of JAK protein" to GO:0042976 * Added general dbxref GOC:tb to synonym activation of JAK protein of GO:0042976 * Added general dbxref GOC:dph to synonym activation of JAK protein of GO:0042976 * Changed synonym scope of GO:0042976 from "Related" to "Exact" * Changed name of GO:0042977 from "activation of JAK2 protein" to "activation of JAK2 kinase activity" * Added synonym "activation of JAK2 protein" to GO:0042977 * Added general dbxref GOC:tb to synonym activation of JAK2 protein of GO:0042977 * Added general dbxref GOC:dph to synonym activation of JAK2 protein of GO:0042977 * Changed synonym scope of GO:0042977 from "Related" to "Exact" * Changed definition of GO:0050877 from "The processes pertaining to the functions of the nervous system of an organism." to "A organ system process carried out by any of the organs or tissues of neurological system." From gocvs at genome.stanford.edu Mon Apr 7 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Mon, 7 Apr 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 04/07/2008 Message-ID: <200804080430.VAA20386@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.751 by 5.752 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034358 * Created object of type obo:TERM with id GO:0034359 * Created object of type obo:TERM with id GO:0034360 * Created object of type obo:TERM with id GO:0034361 * Created object of type obo:TERM with id GO:0034362 * Created object of type obo:TERM with id GO:0034363 * Created object of type obo:TERM with id GO:0034364 * Created object of type obo:TERM with id GO:0034365 * Created object of type obo:TERM with id GO:0034366 * Created object of type obo:TERM with id GO:0034367 * Created object of type obo:TERM with id GO:0034368 * Created object of type obo:TERM with id GO:0034369 * Created object of type obo:TERM with id GO:0034370 * Created object of type obo:TERM with id GO:0034371 * Created object of type obo:TERM with id GO:0034372 * Created object of type obo:TERM with id GO:0034373 * Created object of type obo:TERM with id GO:0034374 * Created object of type obo:TERM with id GO:0034375 * Created object of type obo:TERM with id GO:0034376 * Created object of type obo:TERM with id GO:0034377 * Created object of type obo:TERM with id GO:0034378 * Created object of type obo:TERM with id GO:0034379 * Created object of type obo:TERM with id GO:0034380 * Created object of type obo:TERM with id GO:0034381 * Created object of type obo:TERM with id GO:0034382 * Created object of type obo:TERM with id GO:0034383 * Created object of type obo:TERM with id GO:0034384 * Created object of type obo:TERM with id GO:0034385 * Populated new object GO:0034358 (macro) * Changed name of GO:0034358 from "" to "plasma lipoprotein particle" * Set definition of GO:0034358 to "A spherical particle with a hydrophobic core of triglycerides and/or cholesterol esters, surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins. Plasma lipoprotein particles transport lipids, which are non-covalently associated with the particles, in the blood or lymph." * Added definition dbxref GOC:expert_pt to GO:0034358 * Added definition dbxref GOC:rl to GO:0034358 * Copied GO:0034358 to GO:0032994 with type OBO_REL:is_a * Copied GO:0034358 to GO:0005615 with type part_of * Assigned namespace "cellular_component" to GO:0034358 * Populated new object GO:0034359 (macro) * Changed name of GO:0034359 from "" to "mature chylomicron" * Set definition of GO:0034359 to "A chylomicron that contains apolipoprotein C2 (APOC2), a cofactor for lipoprotein lipase (LPL) activity, and has a mean diameter of 500 nm and density of 0.95g/ml. Mature chylomicron particles transport exogenous (dietary) lipids from the intestines to other body tissues, via the blood and lymph." * Added definition dbxref GOC:expert_pt to GO:0034359 * Added definition dbxref GOC:mah to GO:0034359 * Added definition dbxref GOC:rl to GO:0034359 * Copied GO:0034359 to GO:0042627 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034359 * Populated new object GO:0034360 (macro) * Changed name of GO:0034360 from "" to "chylomicron remnant" * Set definition of GO:0034360 to "A lipoprotein particle that is derived from a mature chylomicron particle by the removal of triglycerides from the chylomicron core by lipoprotein lipase and the subsequent loss of surface components. It characteristically contains apolipoprotein E (APOE) and is cleared from the blood by the liver." * Added definition dbxref GOC:expert_pt to GO:0034360 * Added definition dbxref GOC:mah to GO:0034360 * Added definition dbxref GOC:rl to GO:0034360 * Copied GO:0034360 to GO:0042627 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034360 * Populated new object GO:0034361 (macro) * Changed name of GO:0034361 from "" to "very-low-density lipoprotein particle" * Set definition of GO:0034361 to "A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver." * Added definition dbxref GOC:expert_pt to GO:0034361 * Added definition dbxref GOC:mah to GO:0034361 * Added definition dbxref GOC:rl to GO:0034361 * Added synonym "very-low-density lipoprotein complex" to GO:0034361 * Changed synonym scope of GO:0034361 from "Related" to "Exact" * Added synonym "VLDL complex" to GO:0034361 * Changed synonym scope of GO:0034361 from "Related" to "Exact" * Added synonym "VLDL particle" to GO:0034361 * Changed synonym scope of GO:0034361 from "Related" to "Exact" * Copied GO:0034361 to GO:0034385 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034361 * Populated new object GO:0034362 (macro) * Changed name of GO:0034362 from "" to "low-density lipoprotein particle" * Set definition of GO:0034362 to "A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triacylglycerol and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver." * Added definition dbxref GOC:expert_pt to GO:0034362 * Added definition dbxref GOC:mah to GO:0034362 * Added definition dbxref GOC:rl to GO:0034362 * Added synonym "LDL complex" to GO:0034362 * Changed synonym scope of GO:0034362 from "Related" to "Exact" * Added synonym "LDL particle" to GO:0034362 * Changed synonym scope of GO:0034362 from "Related" to "Exact" * Added synonym "low-density lipoprotein complex" to GO:0034362 * Changed synonym scope of GO:0034362 from "Related" to "Exact" * Copied GO:0034362 to GO:0034358 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034362 * Populated new object GO:0034363 (macro) * Changed name of GO:0034363 from "" to "intermediate-density lipoprotein particle" * Set definition of GO:0034363 to "A triglyceride-rich lipoprotein particle that typically contains APOB100, APOE and APOCs and has a density of 1.006-1.019 g/ml and a diameter of between 25-30 nm. IDL particles are found in blood and are formed by the delipidation of very-low-density lipoprotein particles (VLDL). IDL particles are removed from blood by the liver, following binding to the APOE receptor, or are converted to low-density lipoprotein (LDL)." * Added definition dbxref GOC:expert_pt to GO:0034363 * Added definition dbxref GOC:mah to GO:0034363 * Added definition dbxref GOC:rl to GO:0034363 * Added synonym "IDL complex" to GO:0034363 * Changed synonym scope of GO:0034363 from "Related" to "Exact" * Added synonym "IDL particle" to GO:0034363 * Changed synonym scope of GO:0034363 from "Related" to "Exact" * Added synonym "intermediate-density lipoprotein complex" to GO:0034363 * Changed synonym scope of GO:0034363 from "Related" to "Exact" * Copied GO:0034363 to GO:0034385 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034363 * Populated new object GO:0034364 (macro) * Changed name of GO:0034364 from "" to "high-density lipoprotein particle" * Set definition of GO:0034364 to "A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process." * Added definition dbxref GOC:expert_pt to GO:0034364 * Added definition dbxref GOC:mah to GO:0034364 * Added definition dbxref GOC:pd to GO:0034364 * Added definition dbxref GOC:rl to GO:0034364 * Added synonym "HDL complex" to GO:0034364 * Changed synonym scope of GO:0034364 from "Related" to "Exact" * Added synonym "HDL particle" to GO:0034364 * Changed synonym scope of GO:0034364 from "Related" to "Exact" * Added synonym "HDL2" to GO:0034364 * Added synonym "HDL3" to GO:0034364 * Added synonym "high-density lipoprotein class complex" to GO:0034364 * Changed synonym scope of GO:0034364 from "Related" to "Exact" * Copied GO:0034364 to GO:0034358 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034364 * Populated new object GO:0034365 (macro) * Changed name of GO:0034365 from "" to "discoidal high-density lipoprotein particle" * Set definition of GO:0034365 to "A newly formed high-density lipoprotein particle; consists of a phospholipid bilayer surrounded by two or more APOA1 molecules. The discoidal HDL particle is formed when lipid-free or lipid-poor APOA1 acquires phospholipids and unesterified cholesterol from either cell membranes or triglyceride-rich lipoproteins (undergoing lipolysis by lipoprotein lipase)." * Added definition dbxref GOC:expert_pt to GO:0034365 * Added definition dbxref GOC:mah to GO:0034365 * Added definition dbxref GOC:rl to GO:0034365 * Added synonym "discoidal HDL" to GO:0034365 * Changed synonym scope of GO:0034365 from "Related" to "Exact" * Added synonym "nascent HDL" to GO:0034365 * Changed synonym scope of GO:0034365 from "Related" to "Exact" * Added synonym "nascent high-density lipoprotein particle" to GO:0034365 * Changed synonym scope of GO:0034365 from "Related" to "Exact" * Copied GO:0034365 to GO:0034364 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034365 * Populated new object GO:0034366 (macro) * Changed name of GO:0034366 from "" to "spherical high-density lipoprotein particle" * Set definition of GO:0034366 to "A mature high-density lipoprotein (HDL) particle, converted from discoidal HDL particles following the esterification of cholesterol in the particle by phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT)." * Added definition dbxref GOC:expert_pt to GO:0034366 * Added definition dbxref GOC:mah to GO:0034366 * Added definition dbxref GOC:rl to GO:0034366 * Added synonym "mature HDL" to GO:0034366 * Changed synonym scope of GO:0034366 from "Related" to "Exact" * Added synonym "mature high-density lipoprotein particle" to GO:0034366 * Changed synonym scope of GO:0034366 from "Related" to "Exact" * Added synonym "spherical HDL" to GO:0034366 * Changed synonym scope of GO:0034366 from "Related" to "Exact" * Copied GO:0034366 to GO:0034364 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034366 * Populated new object GO:0034367 (macro) * Changed name of GO:0034367 from "" to "macromolecular complex remodeling" * Set definition of GO:0034367 to "The acquisition, loss, or modification of molecules within a complex. The remodeling process begins with an existing complex, and ends with an altered complex." * Added definition dbxref GOC:mah to GO:0034367 * Added definition dbxref GOC:rl to GO:0034367 * Copied GO:0034367 to GO:0043170 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034367 * Populated new object GO:0034368 (macro) * Changed name of GO:0034368 from "" to "protein-lipid complex remodeling" * Set definition of GO:0034368 to "The acquisition, loss or modification of a protein or lipid within a protein-lipid complex." * Added definition dbxref GOC:mah to GO:0034368 * Added definition dbxref GOC:rl to GO:0034368 * Copied GO:0034368 to GO:0034367 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034368 * Populated new object GO:0034369 (macro) * Changed name of GO:0034369 from "" to "plasma lipoprotein particle remodeling" * Set definition of GO:0034369 to "The acquisition, loss or modification of a protein or lipid within a plasma lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the esterification of cholesterol by phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT)." * Added definition dbxref GOC:expert_pt to GO:0034369 * Added definition dbxref GOC:mah to GO:0034369 * Added definition dbxref GOC:rl to GO:0034369 * Copied GO:0034369 to GO:0034368 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034369 * Populated new object GO:0034370 (macro) * Changed name of GO:0034370 from "" to "triglyceride-rich lipoprotein particle remodeling" * Set definition of GO:0034370 to "The acquisition, loss or modification of a protein or lipid within a triglyceride-rich lipoprotein particle, including the hydrolysis of triglyceride by lipoprotein lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride from a triglyceride-rich lipoprotein particle." * Added definition dbxref GOC:expert_pt to GO:0034370 * Added definition dbxref GOC:mah to GO:0034370 * Added definition dbxref GOC:rl to GO:0034370 * Copied GO:0034370 to GO:0034369 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034370 * Populated new object GO:0034371 (macro) * Changed name of GO:0034371 from "" to "chylomicron remodeling" * Set definition of GO:0034371 to "The acquisition, loss or modification of a protein or lipid within a chylomicron, including the hydrolysis of triglyceride by lipoprotein lipase and the subsequent loss of free fatty acid." * Added definition dbxref GOC:expert_pt to GO:0034371 * Added definition dbxref GOC:mah to GO:0034371 * Added definition dbxref GOC:rl to GO:0034371 * Added synonym "chylomicron remnant formation" to GO:0034371 * Copied GO:0034371 to GO:0034370 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034371 * Populated new object GO:0034372 (macro) * Changed name of GO:0034372 from "" to "very-low-density lipoprotein particle remodeling" * Set definition of GO:0034372 to "The acquisition, loss or modification of a protein or lipid within a very-low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase or lipoprotein lipase and the subsequent loss of free fatty acid." * Added definition dbxref GOC:expert_pt to GO:0034372 * Added definition dbxref GOC:mah to GO:0034372 * Added definition dbxref GOC:rl to GO:0034372 * Added synonym "IDL formation" to GO:0034372 * Added synonym "intermediate-density lipoprotein particle formation" to GO:0034372 * Added synonym "VLDL remodeling" to GO:0034372 * Changed synonym scope of GO:0034372 from "Related" to "Exact" * Copied GO:0034372 to GO:0034370 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034372 * Populated new object GO:0034373 (macro) * Changed name of GO:0034373 from "" to "intermediate-density lipoprotein particle remodeling" * Set definition of GO:0034373 to "The acquisition, loss or modification of a protein or lipid within an intermediate-density lipoprotein particle." * Added definition dbxref GOC:expert_pt to GO:0034373 * Added definition dbxref GOC:mah to GO:0034373 * Added definition dbxref GOC:rl to GO:0034373 * Added synonym "IDL remodeling" to GO:0034373 * Changed synonym scope of GO:0034373 from "Related" to "Exact" * Added synonym "LDL formation" to GO:0034373 * Added synonym "low-density lipoprotein particle formation" to GO:0034373 * Copied GO:0034373 to GO:0034370 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034373 * Populated new object GO:0034374 (macro) * Changed name of GO:0034374 from "" to "low-density lipoprotein particle remodeling" * Set definition of GO:0034374 to "The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL." * Added definition dbxref GOC:expert_pt to GO:0034374 * Added definition dbxref GOC:mah to GO:0034374 * Added definition dbxref GOC:rl to GO:0034374 * Added synonym "LDL remodeling" to GO:0034374 * Changed synonym scope of GO:0034374 from "Related" to "Exact" * Copied GO:0034374 to GO:0034369 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034374 * Populated new object GO:0034375 (macro) * Changed name of GO:0034375 from "" to "high-density lipoprotein particle remodeling" * Set definition of GO:0034375 to "The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL." * Added definition dbxref GOC:expert_pt to GO:0034375 * Added definition dbxref GOC:mah to GO:0034375 * Added definition dbxref GOC:rl to GO:0034375 * Added synonym "HDL remodeling" to GO:0034375 * Changed synonym scope of GO:0034375 from "Related" to "Exact" * Copied GO:0034375 to GO:0034369 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034375 * Populated new object GO:0034376 (macro) * Changed name of GO:0034376 from "" to "conversion of discoidal high-density lipoprotein to spherical high-density lipoprotein" * Set definition of GO:0034376 to "The process by which a discoidal high-density lipoprotein (HDL) particle acquires additional lipid or protein molecules, and cholesterol in the particle is converted to tightly bound cholesterol esters by the action of phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT), resulting in the formation of a spherical HDL particle." * Added definition dbxref GOC:pd; GOC:mah to GO:0034376 * Added synonym "conversion of discoidal HDL to spherical HDL" to GO:0034376 * Changed synonym scope of GO:0034376 from "Related" to "Exact" * Added synonym "discoidal HDL remodeling" to GO:0034376 * Added synonym "discoidal high-density lipoprotein remodeling" to GO:0034376 * Copied GO:0034376 to GO:0034377 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034376 * Populated new object GO:0034377 (macro) * Changed name of GO:0034377 from "" to "plasma lipoprotein particle assembly" * Set definition of GO:0034377 to "The aggregation and arrangement of proteins and lipids to form a plasma lipoprotein particle." * Added definition dbxref GOC:mah to GO:0034377 * Copied GO:0034377 to GO:0065005 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034377 * Populated new object GO:0034378 (macro) * Changed name of GO:0034378 from "" to "chylomicron assembly" * Set definition of GO:0034378 to "The aggregation and arrangement of proteins and lipids in the intestine to form a chylomicron." * Added definition dbxref GOC:mah to GO:0034378 * Copied GO:0034378 to GO:0034377 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034378 * Populated new object GO:0034379 (macro) * Changed name of GO:0034379 from "" to "very-low-density lipoprotein particle assembly" * Set definition of GO:0034379 to "The aggregation and arrangement of proteins and lipids in the liver to form a very-low-density lipoprotein particle" * Added definition dbxref GOC:mah to GO:0034379 * Added synonym "VLDL assembly" to GO:0034379 * Changed synonym scope of GO:0034379 from "Related" to "Exact" * Copied GO:0034379 to GO:0034377 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034379 * Populated new object GO:0034380 (macro) * Changed name of GO:0034380 from "" to "high-density lipoprotein particle assembly" * Set definition of GO:0034380 to "The aggregation and arrangement of proteins and lipids to form a high-density lipoprotein particle." * Added definition dbxref GOC:mah to GO:0034380 * Added synonym "HDL assembly" to GO:0034380 * Changed synonym scope of GO:0034380 from "Related" to "Exact" * Copied GO:0034380 to GO:0034377 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034380 * Populated new object GO:0034381 (macro) * Changed name of GO:0034381 from "" to "lipoprotein particle clearance" * Set definition of GO:0034381 to "The process by which a lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." * Added definition dbxref GOC:mah to GO:0034381 * Copied GO:0034381 to GO:0032984 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034381 * Populated new object GO:0034382 (macro) * Changed name of GO:0034382 from "" to "chylomicron remnant clearance" * Set definition of GO:0034382 to "The process by which a chylomicron remnant is removed from the blood via receptor-mediated endocytosis into liver cells and its constituent parts degraded." * Added definition dbxref GOC:mah to GO:0034382 * Added definition dbxref GOC:pd to GO:0034382 * Copied GO:0034382 to GO:0034381 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034382 * Populated new object GO:0034383 (macro) * Changed name of GO:0034383 from "" to "low-density lipoprotein particle clearance" * Set definition of GO:0034383 to "The process by which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." * Added definition dbxref GOC:mah to GO:0034383 * Added synonym "LDL clearance" to GO:0034383 * Changed synonym scope of GO:0034383 from "Related" to "Exact" * Copied GO:0034383 to GO:0034381 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034383 * Populated new object GO:0034384 (macro) * Changed name of GO:0034384 from "" to "high-density lipoprotein particle clearance" * Set definition of GO:0034384 to "The process by which a high-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." * Added definition dbxref GOC:mah to GO:0034384 * Added synonym "HDL clearance" to GO:0034384 * Changed synonym scope of GO:0034384 from "Related" to "Exact" * Copied GO:0034384 to GO:0034381 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034384 * Populated new object GO:0034385 (macro) * Changed name of GO:0034385 from "" to "triglyceride-rich lipoprotein particle" * Set definition of GO:0034385 to "A plasma lipoprotein particle that has a hydrophobic core enriched in triglycerides surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins. Triglyceride-rich lipoproteinparticles transport lipids, which are non-covalently associated with the particles, in the blood." * Added definition dbxref GOC:mah to GO:0034385 * Added definition dbxref GOC:rl to GO:0034385 * Copied GO:0034385 to GO:0034358 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034385 * Deleted GO:0032984 --OBO_REL:is_a--> GO:0022411 * Copied GO:0032984 to GO:0043170 with type OBO_REL:is_a * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Changed definition of GO:0042627 from "A particle composed of a central core of triglycerides surrounded by a protein-phospholipid coating. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues." to "A large lipoprotein particle (diameter 75-1200 nm) composed of a central core of triglycerides and cholesterol surrounded by a protein-phospholipid coating. The proteins include one molecule of apolipoprotein B-48 and may include a variety of apolipoproteins, including APOAs, APOCs and APOE. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues." * Added definition dbxref GOC:rl to GO:0042627 * Deleted GO:0042627 --OBO_REL:is_a--> GO:0044421 * Copied GO:0042627 to GO:0034358 with type OBO_REL:is_a * Deleted GO:0065003 --OBO_REL:is_a--> GO:0022607 From gocvs at genome.stanford.edu Tue Apr 8 21:30:50 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Tue, 8 Apr 2008 21:30:50 -0700 (PDT) Subject: [Go-diff] GO update 04/08/2008 Message-ID: <200804090430.VAA01185@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.752 by 5.753 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034386 * Created object of type obo:TERM with id GO:0034387 * Created object of type obo:TERM with id GO:0034388 * Created object of type obo:TERM with id GO:0034389 * Created object of type obo:TERM with id GO:0034390 * Created object of type obo:TERM with id GO:0034391 * Created object of type obo:TERM with id GO:0034392 * Created object of type obo:TERM with id GO:0034393 * Created object of type obo:TERM with id GO:0034394 * Created object of type obo:TERM with id GO:0034395 * Created object of type obo:TERM with id GO:0034396 * Populated new object GO:0034386 (macro) * Changed name of GO:0034386 from "" to "4-aminobutyrate:2-oxoglutarate transaminase activity" * Set definition of GO:0034386 to "Catalysis of the reaction: 4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate." * Added definition dbxref EC:2.6.1.19 to GO:0034386 * Added definition dbxref GOC:mah to GO:0034386 * Added synonym "4-aminobutanoate:2-oxoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym 4-aminobutanoate:2-oxoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "4-aminobutyrate-2-ketoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym 4-aminobutyrate-2-ketoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "4-aminobutyrate-2-oxoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym 4-aminobutyrate-2-oxoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "4-aminobutyrate-2-oxoglutarate transaminase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym 4-aminobutyrate-2-oxoglutarate transaminase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "4-aminobutyric acid 2-ketoglutaric acid aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym 4-aminobutyric acid 2-ketoglutaric acid aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "GABA-2-oxoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym GABA-2-oxoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "GABA-2-oxoglutarate transaminase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym GABA-2-oxoglutarate transaminase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "GABA-alpha-ketoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym GABA-alpha-ketoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "GABA-alpha-ketoglutarate transaminase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym GABA-alpha-ketoglutarate transaminase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "GABA-alpha-ketoglutaric acid transaminase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym GABA-alpha-ketoglutaric acid transaminase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "GABA-alpha-oxoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym GABA-alpha-oxoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "GABA-oxoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym GABA-oxoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "GABA-oxoglutarate transaminase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym GABA-oxoglutarate transaminase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "gamma-aminobutyrate-alpha-ketoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym gamma-aminobutyrate-alpha-ketoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "gamma-aminobutyrate-alpha-ketoglutarate transaminase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym gamma-aminobutyrate-alpha-ketoglutarate transaminase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "gamma-aminobutyrate:alpha-oxoglutarate aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym gamma-aminobutyrate:alpha-oxoglutarate aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "gamma-aminobutyric acid-2-oxoglutarate transaminase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym gamma-aminobutyric acid-2-oxoglutarate transaminase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "gamma-aminobutyric acid-alpha-ketoglutarate transaminase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym gamma-aminobutyric acid-alpha-ketoglutarate transaminase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Added synonym "gamma-aminobutyric acid-alpha-ketoglutaric acid aminotransferase activity" to GO:0034386 * Added general dbxref EC:2.6.1.19 to synonym gamma-aminobutyric acid-alpha-ketoglutaric acid aminotransferase activity of GO:0034386 * Changed synonym scope of GO:0034386 from "Related" to "Exact" * Copied GO:0034386 to GO:0003867 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034386 * Populated new object GO:0034387 (macro) * Changed name of GO:0034387 from "" to "4-aminobutyrate:pyruvate transaminase activity" * Set definition of GO:0034387 to "Catalysis of the reaction: 4-aminobutanoate + pyruvate = succinate semialdehyde + alanine." * Added definition dbxref EC:2.6.1.19 to GO:0034387 * Added definition dbxref GOC:mah to GO:0034387 * Added synonym "gamma-aminobutyric acid pyruvate transaminase activity" to GO:0034387 * Added general dbxref EC:2.6.1.19 to synonym gamma-aminobutyric acid pyruvate transaminase activity of GO:0034387 * Changed synonym scope of GO:0034387 from "Related" to "Exact" * Copied GO:0034387 to GO:0003867 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034387 * Populated new object GO:0034388 (macro) * Changed name of GO:0034388 from "" to "Pwp2p-containing subcomplex of 90S preribosome" * Added comment "Note that the term name uses Saccharomyces gene product names because no other names have yet arisen for this complex; the term nevertheless can be used for analogous complexes in other eukaryotes, and the name can be changed if better wording is found." * Set definition of GO:0034388 to "A protein complex that forms a subcomplex of the 90S preribosome and can interact directly with the 5' External Transcribed Spacer (ETS) of the full length pre-rRNA transcript. In S. cerevisiae, it sediments at 25-30 S and is composed of Pwp2p, Dip2p, Utp21p, Utp13p, Utp18p, and Utp6p." * Added definition dbxref GOC:krc to GO:0034388 * Added definition dbxref PMID:15231838 to GO:0034388 * Added synonym "25-30 S subcomplex of 90S preribosome" to GO:0034388 * Changed synonym scope of GO:0034388 from "Related" to "Exact" * Copied GO:0034388 to GO:0044452 with type OBO_REL:is_a * Copied GO:0034388 to GO:0030686 with type part_of * Copied GO:0034388 to GO:0043234 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034388 * Populated new object GO:0034389 (macro) * Changed name of GO:0034389 from "" to "lipid particle organization and biogenesis" * Set definition of GO:0034389 to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a lipid particle." * Added definition dbxref PMID:18093937 to GO:0034389 * Added definition dbxref PMID:18250201 to GO:0034389 * Added synonym "adiposome organization and biogenesis" to GO:0034389 * Changed synonym scope of GO:0034389 from "Related" to "Exact" * Added synonym "lipid body organization and biogenesis" to GO:0034389 * Changed synonym scope of GO:0034389 from "Related" to "Exact" * Added synonym "lipid droplet organization and biogenesis" to GO:0034389 * Changed synonym scope of GO:0034389 from "Related" to "Exact" * Added synonym "lipid particle organisation and biogenesis" to GO:0034389 * Changed synonym scope of GO:0034389 from "Related" to "Exact" * Copied GO:0034389 to GO:0006996 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034389 * Populated new object GO:0034390 (macro) * Changed name of GO:0034390 from "" to "smooth muscle cell apoptosis" * Set definition of GO:0034390 to "The process of apoptosis in smooth muscle cells. Smooth muscle consists of non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels." * Added definition dbxref CL:0000192 to GO:0034390 * Added definition dbxref GOC:mah to GO:0034390 * Added definition dbxref GOC:rl to GO:0034390 * Added synonym "apoptosis of smooth muscle cells" to GO:0034390 * Changed synonym scope of GO:0034390 from "Related" to "Exact" * Added synonym "programmed cell death of smooth muscle cells by apoptosis" to GO:0034390 * Changed synonym scope of GO:0034390 from "Related" to "Exact" * Added synonym "programmed cell death, smooth muscle cells" to GO:0034390 * Changed synonym scope of GO:0034390 from "Related" to "Exact" * Added synonym "SMC apoptosis" to GO:0034390 * Changed synonym scope of GO:0034390 from "Related" to "Exact" * Added synonym "smooth muscle cell programmed cell death by apoptosis" to GO:0034390 * Changed synonym scope of GO:0034390 from "Related" to "Exact" * Copied GO:0034390 to GO:0006915 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034390 * Populated new object GO:0034391 (macro) * Changed name of GO:0034391 from "" to "regulation of smooth muscle cell apoptosis" * Set definition of GO:0034391 to "Any process that modulates the frequency, rate, or extent of smooth muscle cell apoptosis." * Added definition dbxref GOC:rl to GO:0034391 * Added synonym "regulation of SMC apoptosis" to GO:0034391 * Changed synonym scope of GO:0034391 from "Related" to "Exact" * Copied GO:0034391 to GO:0042981 with type OBO_REL:is_a * Copied GO:0034391 to GO:0034390 with type regulates * Assigned namespace "biological_process" to GO:0034391 * Populated new object GO:0034392 (macro) * Changed name of GO:0034392 from "" to "negative regulation of smooth muscle cell apoptosis" * Set definition of GO:0034392 to "Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptosis." * Added definition dbxref GOC:rl to GO:0034392 * Added synonym "down regulation of smooth muscle cell apoptosis" to GO:0034392 * Changed synonym scope of GO:0034392 from "Related" to "Exact" * Added synonym "down-regulation of smooth muscle cell apoptosis" to GO:0034392 * Changed synonym scope of GO:0034392 from "Related" to "Exact" * Added synonym "downregulation of smooth muscle cell apoptosis" to GO:0034392 * Changed synonym scope of GO:0034392 from "Related" to "Exact" * Added synonym "inhibition of smooth muscle cell apoptosis" to GO:0034392 * Changed synonym scope of GO:0034392 from "Related" to "Narrow" * Added synonym "negative regulation of SMC apoptosis" to GO:0034392 * Changed synonym scope of GO:0034392 from "Related" to "Exact" * Copied GO:0034392 to GO:0034390 with type negatively_regulates * Copied GO:0034392 to GO:0034391 with type OBO_REL:is_a * Copied GO:0034392 to GO:0043066 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034392 * Populated new object GO:0034393 (macro) * Changed name of GO:0034393 from "" to "positive regulation of smooth muscle cell apoptosis" * Set definition of GO:0034393 to "Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptosis." * Added definition dbxref GOC:rl to GO:0034393 * Added synonym "activation of smooth muscle cell apoptosis" to GO:0034393 * Changed synonym scope of GO:0034393 from "Related" to "Narrow" * Added synonym "positive regulation of SMC apoptosis" to GO:0034393 * Changed synonym scope of GO:0034393 from "Related" to "Exact" * Added synonym "stimulation of smooth muscle cell apoptosis" to GO:0034393 * Changed synonym scope of GO:0034393 from "Related" to "Narrow" * Added synonym "up regulation of smooth muscle cell apoptosis" to GO:0034393 * Changed synonym scope of GO:0034393 from "Related" to "Exact" * Added synonym "up-regulation of smooth muscle cell apoptosis" to GO:0034393 * Changed synonym scope of GO:0034393 from "Related" to "Exact" * Added synonym "upregulation of smooth muscle cell apoptosis" to GO:0034393 * Changed synonym scope of GO:0034393 from "Related" to "Exact" * Copied GO:0034393 to GO:0043065 with type OBO_REL:is_a * Copied GO:0034393 to GO:0034390 with type positively_regulates * Copied GO:0034393 to GO:0034391 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034393 * Populated new object GO:0034394 (macro) * Changed name of GO:0034394 from "" to "protein localization at cell surface" * Set definition of GO:0034394 to "A process by which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane." * Added definition dbxref GOC:mah to GO:0034394 * Copied GO:0034394 to GO:0008104 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034394 * Populated new object GO:0034395 (macro) * Changed name of GO:0034395 from "" to "regulation of transcription from RNA polymerase II promoter in response to iron" * Added comment "This term was added by GO_REF:0000021." * Set definition of GO:0034395 to "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an iron stimulus." * Added definition dbxref GOC:mah to GO:0034395 * Added synonym "regulation of specific transcription from RNA polymerase II promoter in response to iron" to GO:0034395 * Changed synonym scope of GO:0034395 from "Related" to "Exact" * Copied GO:0034395 to GO:0010039 with type OBO_REL:is_a * Copied GO:0034395 to GO:0010551 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034395 * Populated new object GO:0034396 (macro) * Changed name of GO:0034396 from "" to "negative regulation of transcription from RNA polymerase II promoter in response to iron" * Set definition of GO:0034396 to "Any process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter in response to an iron stimulus." * Added definition dbxref GOC:mah to GO:0034396 * Added synonym "down regulation of transcription from RNA polymerase II promoter in response to iron" to GO:0034396 * Changed synonym scope of GO:0034396 from "Related" to "Exact" * Added synonym "down-regulation of transcription from RNA polymerase II promoter in response to iron" to GO:0034396 * Changed synonym scope of GO:0034396 from "Related" to "Exact" * Added synonym "downregulation of transcription from RNA polymerase II promoter in response to iron" to GO:0034396 * Changed synonym scope of GO:0034396 from "Related" to "Exact" * Added synonym "inhibition of transcription from RNA polymerase II promoter in response to iron" to GO:0034396 * Changed synonym scope of GO:0034396 from "Related" to "Narrow" * Added synonym "negative regulation of transcription from Pol II promoter in response to iron" to GO:0034396 * Changed synonym scope of GO:0034396 from "Related" to "Exact" * Copied GO:0034396 to GO:0034395 with type OBO_REL:is_a * Copied GO:0034396 to GO:0010553 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034396 * Deleted definition dbxref ISBN:0721662544 from GO:0000093 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0000093 * Deleted definition dbxref ISBN:0721662544 from GO:0001756 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0001756 * Deleted definition dbxref ISBN:0721662544 from GO:0001763 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0001763 * Deleted definition dbxref ISBN:0721662544 from GO:0001822 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0001822 * Deleted definition dbxref ISBN:0721662544 from GO:0001823 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0001823 * Changed synonym scope of GO:0001898 from "Related" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0003823 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0003823 * Changed definition of GO:0003867 from "Catalysis of the reaction: 4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate." to "Catalysis of the reaction: 4-aminobutanoate + amino group acceptor = succinate semialdehyde + amino acid." * Added definition dbxref GOC:mah to GO:0003867 * Deleted synonym "4-aminobutanoate:2-oxoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "4-aminobutyrate-2-ketoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "4-aminobutyrate-2-oxoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "4-aminobutyrate-2-oxoglutarate transaminase activity" from GO:0003867 * Deleted synonym "4-aminobutyric acid 2-ketoglutaric acid aminotransferase activity" from GO:0003867 * Changed synonym scope of GO:0003867 from "Broad" to "Related" * Changed synonym scope of GO:0003867 from "Exact" to "Related" * Changed synonym scope of GO:0003867 from "Exact" to "Related" * Deleted synonym "GABA-2-oxoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "GABA-2-oxoglutarate transaminase activity" from GO:0003867 * Deleted synonym "GABA-alpha-ketoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "GABA-alpha-ketoglutarate transaminase activity" from GO:0003867 * Deleted synonym "GABA-alpha-ketoglutaric acid transaminase activity" from GO:0003867 * Deleted synonym "GABA-alpha-oxoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "GABA-oxoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "GABA-oxoglutarate transaminase activity" from GO:0003867 * Deleted synonym "gamma-aminobutyrate-alpha-ketoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "gamma-aminobutyrate-alpha-ketoglutarate transaminase activity" from GO:0003867 * Deleted synonym "gamma-aminobutyrate:alpha-oxoglutarate aminotransferase activity" from GO:0003867 * Deleted synonym "gamma-aminobutyric acid pyruvate transaminase activity" from GO:0003867 * Deleted synonym "gamma-aminobutyric acid-2-oxoglutarate transaminase activity" from GO:0003867 * Deleted synonym "gamma-aminobutyric acid-alpha-ketoglutarate transaminase activity" from GO:0003867 * Deleted synonym "gamma-aminobutyric acid-alpha-ketoglutaric acid aminotransferase activity" from GO:0003867 * Changed synonym scope of GO:0004445 from "Broad" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0005522 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0005522 * Deleted definition dbxref ISBN:0721662544 from GO:0005549 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0005549 * Changed synonym scope of GO:0005802 from "Related" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0005901 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0005901 * Deleted definition dbxref ISBN:0721662544 from GO:0007552 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0007552 * Deleted definition dbxref ISBN:0721662544 from GO:0007612 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0007612 * Deleted definition dbxref ISBN:0721662544 from GO:0007620 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0007620 * Deleted definition dbxref ISBN:0721662544 from GO:0008238 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0008238 * Deleted definition dbxref ISBN:0721662544 from GO:0008305 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0008305 * Deleted definition dbxref ISBN:0721662544 from GO:0008373 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0008373 * Deleted definition dbxref ISBN:0721662544 from GO:0008395 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0008395 * Deleted definition dbxref ISBN:0721662544 from GO:0008431 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0008431 * Deleted definition dbxref ISBN:0721662544 from GO:0009887 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0009887 * Changed synonym scope of GO:0010342 from "Related" to "Exact" * Changed synonym scope of GO:0010362 from "Related" to "Exact" * Changed synonym scope of GO:0010497 from "Related" to "Exact" * Changed synonym scope of GO:0010497 from "Related" to "Exact" * Changed synonym scope of GO:0010497 from "Related" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0015233 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0015233 * Deleted definition dbxref ISBN:0721662544 from GO:0015663 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0015663 * Deleted definition dbxref ISBN:0721662544 from GO:0015887 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0015887 * Deleted definition dbxref ISBN:0721662544 from GO:0015890 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0015890 * Deleted definition dbxref ISBN:0721662544 from GO:0015929 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0015929 * Deleted definition dbxref ISBN:0721662544 from GO:0015939 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0015939 * Deleted definition dbxref ISBN:0721662544 from GO:0015940 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0015940 * Deleted definition dbxref ISBN:0721662544 from GO:0015941 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0015941 * Deleted definition dbxref ISBN:0721662544 from GO:0016030 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0016030 * Deleted definition dbxref ISBN:0721662544 from GO:0016783 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0016783 * Deleted definition dbxref ISBN:0721662544 from GO:0017106 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0017106 * Deleted definition dbxref ISBN:0721662544 from GO:0017166 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0017166 * Deleted definition dbxref ISBN:0721662544 from GO:0018864 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0018864 * Deleted definition dbxref ISBN:0721662544 from GO:0018874 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0018874 * Deleted definition dbxref ISBN:0721662544 from GO:0018891 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0018891 * Deleted definition dbxref ISBN:0721662544 from GO:0019033 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0019033 * Deleted definition dbxref ISBN:0721662544 from GO:0019487 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0019487 * Deleted definition dbxref ISBN:0721662544 from GO:0019634 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0019634 * Changed synonym scope of GO:0021703 from "Related" to "Exact" * Changed synonym scope of GO:0021703 from "Related" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0030416 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0030416 * Changed definition of GO:0031083 from "A protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. Many of the protein subunits are conserved between mouse and human; the mouse complx contains the Pallidin, Muted, Cappuccino, Dysbindin, Sapin, BLOS1, BLOS2, AND BLOS3 proteins." to "A protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. Many of the protein subunits are conserved between mouse and human; the mouse complex contains the Pallidin, Muted, Cappuccino, Dysbindin, Snapin, BLOS1, BLOS2, AND BLOS3 proteins." * Changed synonym scope of GO:0031443 from "Related" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0032274 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0032274 * Changed synonym scope of GO:0032538 from "Related" to "Exact" * Changed synonym scope of GO:0032540 from "Related" to "Exact" * Changed synonym scope of GO:0033173 from "Related" to "Exact" * Changed definition of GO:0033706 from "Catalysis of the reactions: L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+.shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+." to "Catalysis of the reactions: L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+ and shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+." * Changed definition of GO:0033715 from "Catalysis of the reactions: inosine + O2 = 9-riburonosylhypoxanthine + 2 H2O.(1a) 2 inosine + O2 = 2 5'-dehydroinosine + 2 H2O.(1b) 2 5'-dehydroinosine + O2 = 2 9-riburonosylhypoxanthine + 2 H2O." to "Catalysis of the reactions: inosine + O2 = 9-riburonosylhypoxanthine + 2 H2O and (1a) 2 inosine + O2 = 2 5'-dehydroinosine + 2 H2O and (1b) 2 5'-dehydroinosine + O2 = 2 9-riburonosylhypoxanthine + 2 H2O." * Changed definition of GO:0033716 from "Catalysis of the reactions: adenosine + 2 O2 = 9-riburonosyladenine + 2 H2O2.(1a) adenosine + O2 = 5'-dehydroadenosine + H2O2.(1b) 5'-dehydroadenosine + O2 = 9-riburonosyladenine + H2O2." to "Catalysis of the reactions: adenosine + 2 O2 = 9-riburonosyladenine + 2 H2O2, (1a) adenosine + O2 = 5'-dehydroadenosine + H2O2 and (1b) 5'-dehydroadenosine + O2 = 9-riburonosyladenine + H2O2." * Changed definition of GO:0033718 from "Catalysis of the reactions: pyranose + acceptor = 2-dehydropyranose (or 3-dehydropyranose or 2,3-didehydropyranose) + reduced acceptor.a pyranoside + acceptor = a 3-dehydropyranoside (or 3,4-didehydropyranoside) + reduced acceptor." to "Catalysis of the reactions: pyranose + acceptor = 2-dehydropyranose (or 3-dehydropyranose or 2,3-didehydropyranose) + reduced acceptor and a pyranoside + acceptor = a 3-dehydropyranoside (or 3,4-didehydropyranoside) + reduced acceptor." * Changed definition of GO:0033740 from "Catalysis of the reactions: hydroxylamine + NH3 = hydrazine + H2O.hydrazine + acceptor = N2 + reduced acceptor." to "Catalysis of the reactions: hydroxylamine + NH3 = hydrazine + H2O and hydrazine + acceptor = N2 + reduced acceptor." * Changed definition of GO:0033758 from "Catalysis of the reactions: deoxyamidinoproclavaminate + 2-oxoglutarate + O2 = amidinoproclavaminate + succinate + CO2 + H2O.proclavaminate + 2-oxoglutarate + O2 = dihydroclavaminate + succinate + CO2 + 2 H2O.dihydroclavaminate + 2-oxoglutarate + O2 = clavaminate + succinate + CO2 + 2 H2O." to "Catalysis of the reactions: deoxyamidinoproclavaminate + 2-oxoglutarate + O2 = amidinoproclavaminate + succinate + CO2 + H2O and proclavaminate + 2-oxoglutarate + O2 = dihydroclavaminate + succinate + CO2 + 2 H2O and dihydroclavaminate + 2-oxoglutarate + O2 = clavaminate + succinate + CO2 + 2 H2O." * Changed definition of GO:0033761 from "Catalysis of the reactions: mugineic acid + 2-oxoglutarate + O2 = 3-epihydroxymugineic acid + succinate + CO2.2'-deoxymugineic acid + 2-oxoglutarate + O2 = 3-epihydroxy-2'-deoxymugineic acid + succinate + CO2." to "Catalysis of the reactions: mugineic acid + 2-oxoglutarate + O2 = 3-epihydroxymugineic acid + succinate + CO2 and 2'-deoxymugineic acid + 2-oxoglutarate + O2 = 3-epihydroxy-2'-deoxymugineic acid + succinate + CO2." * Changed definition of GO:0033772 from "Catalysis of the reactions: a flavanone + NADPH + H+ + O2 = a 3'-hydroxyflavanone + NADP+ + H2O.a 3'-hydroxyflavanone + NADPH + H+ + O2 = a 3',5'-dihydroxyflavanone + NADP+ + H2O." to "Catalysis of the reactions: a flavanone + NADPH + H+ + O2 = a 3'-hydroxyflavanone + NADP+ + H2O and a 3'-hydroxyflavanone + NADPH + H+ + O2 = a 3',5'-dihydroxyflavanone + NADP+ + H2O." * Changed definition of GO:0033780 from "Catalysis of the reactions: taurochenodeoxycholate + NADPH + H+ + O2 = taurohyocholate + NADP+ + H2O.lithocholate + NADPH + H+ + O2 = hyodeoxycholate + NADP+ + H2O." to "Catalysis of the reactions: taurochenodeoxycholate + NADPH + H+ + O2 = taurohyocholate + NADP+ + H2O and lithocholate + NADPH + H+ + O2 = hyodeoxycholate + NADP+ + H2O." * Changed definition of GO:0033792 from "Catalysis of the reactions: deoxycholate + FAD + H2O = cholate + FADH2.lithocholate + FAD + H2O = chenodeoxycholate + FADH2." to "Catalysis of the reactions: deoxycholate + FAD + H2O = cholate + FADH2 and lithocholate + FAD + H2O = chenodeoxycholate + FADH2." * Changed definition of GO:0033793 from "Catalysis of the reactions: 2',4,4',6'-tetrahydroxychalcone + O2 = aureusidin + H2O.2',3,4,4',6'-pentahydroxychalcone + 1/2 O2 = aureusidin + H2O." to "Catalysis of the reactions: 2',4,4',6'-tetrahydroxychalcone + O2 = aureusidin + H2O and 2',3,4,4',6'-pentahydroxychalcone + 1/2 O2 = aureusidin + H2O." * Changed definition of GO:0033804 from "Catalysis of the reactions: S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine.S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine." to "Catalysis of the reactions: S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine and S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine." * Changed definition of GO:0033805 from "Catalysis of the reactions: S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine.S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine." to "Catalysis of the reactions: S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine and S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine." * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Changed definition of GO:0033963 from "Catalysis of the reactions: 5,6alpha-epoxy-5alpha-cholestan-3beta-ol + H2O = cholestane-3beta-5alpha,6beta-triol.5,6beta-epoxy-5beta-cholestan-3beta-ol + H2O = cholestane-3beta-5alpha,6beta-triol." to "Catalysis of the reactions: 5,6alpha-epoxy-5alpha-cholestan-3beta-ol + H2O = cholestane-3beta-5alpha,6beta-triol and 5,6beta-epoxy-5beta-cholestan-3beta-ol + H2O = cholestane-3beta-5alpha,6beta-triol." * Changed definition of GO:0033976 from "Catalysis of the reactions: (S)-2-haloacid + H2O = (R)-2-hydroxyacid + halide.(R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide." to "Catalysis of the reactions: (S)-2-haloacid + H2O = (R)-2-hydroxyacid + halide and (R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide." * Changed definition of GO:0033977 from "Catalysis of the reactions: (S)-2-haloacid + H2O = (S)-2-hydroxyacid + halide.(R)-2-haloacid + H2O = (R)-2-hydroxyacid + halide." to "Catalysis of the reactions: (S)-2-haloacid + H2O = (S)-2-hydroxyacid + halide and (R)-2-haloacid + H2O = (R)-2-hydroxyacid + halide." * Changed definition of GO:0033991 from "Catalysis of the reactions: 1,5-anhydro-D-fructose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one + H2O (overall reaction).(1a) 1,5-anhydro-D-fructose = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose + H2O.(1b) 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one." to "Catalysis of the reactions: 1,5-anhydro-D-fructose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one + H2O (overall reaction), (1a) 1,5-anhydro-D-fructose = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose + H2O and (1b) 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one." * Changed definition of GO:0034004 from "Catalysis of the reactions: 2-trans,6-trans-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate.2-trans,6-trans-farnesyl diphosphate = (-)-(7S)-germacrene D + diphosphate." to "Catalysis of the reactions: 2-trans,6-trans-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate and 2-trans,6-trans-farnesyl diphosphate = (-)-(7S)-germacrene D + diphosphate." * Changed definition of GO:0034019 from "Catalysis of the reactions: violaxanthin = capsorubin.antheraxanthin = capsanthin." to "Catalysis of the reactions: violaxanthin = capsorubin and antheraxanthin = capsanthin." * Copied GO:0034351 to GO:0034391 with type OBO_REL:is_a * Copied GO:0034352 to GO:0034391 with type OBO_REL:is_a * Changed definition of GO:0034357 from "A membrane enriched in complexes formed of reaction centers, accessory pigments and electron carriers, in which photosynthetic reactions take place." to "A membrane enriched in complexes formed of reaction centers, accessory pigments and electron carriers, in which photosynthetic reactions take place." * Deleted definition dbxref GOC:pd; GOC:mah from GO:0034376 * Added definition dbxref GOC:mah to GO:0034376 * Added definition dbxref GOC:pd to GO:0034376 * Changed definition of GO:0034379 from "The aggregation and arrangement of proteins and lipids in the liver to form a very-low-density lipoprotein particle" to "The aggregation and arrangement of proteins and lipids in the liver to form a very-low-density lipoprotein particle." * Deleted definition dbxref ISBN:0721662544 from GO:0035265 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0035265 * Deleted definition dbxref ISBN:0721662544 from GO:0042581 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0042581 * Deleted definition dbxref ISBN:0721662544 from GO:0042600 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0042600 * Deleted definition dbxref ISBN:0721662544 from GO:0042698 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0042698 * Deleted definition dbxref ISBN:0721662544 from GO:0042919 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0042919 * Deleted definition dbxref ISBN:0721662544 from GO:0042925 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0042925 * Changed synonym scope of GO:0043424 from "Related" to "Exact" * Changed definition of GO:0045549 from "Catalysis of the reactions: a 9-cis-epoxycarotenoid + O2 = 2-cis,4-trans-xanthoxin + a 12'-apo-carotenal.9-cis-violaxanthin + O2 = 2-cis,4-trans-xanthoxin + (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al.9'-cis-neoxanthin + O2 = 2-cis,4-trans-xanthoxin + (3S,5R,6R)-5,6-dihydroxy-6,7-didehydro-5,6-dihydro-12'-apo-beta-caroten-12'-al." to "Catalysis of the reactions: a 9-cis-epoxycarotenoid + O2 = 2-cis,4-trans-xanthoxin + a 12'-apo-carotenal and 9-cis-violaxanthin + O2 = 2-cis,4-trans-xanthoxin + (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al and 9'-cis-neoxanthin + O2 = 2-cis,4-trans-xanthoxin + (3S,5R,6R)-5,6-dihydroxy-6,7-didehydro-5,6-dihydro-12'-apo-beta-caroten-12'-al." * Deleted definition dbxref ISBN:0721662544 from GO:0046581 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046581 * Deleted definition dbxref ISBN:0721662544 from GO:0046678 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046678 * Deleted definition dbxref ISBN:0721662544 from GO:0046680 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046680 * Deleted definition dbxref ISBN:0721662544 from GO:0046681 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046681 * Deleted definition dbxref ISBN:0721662544 from GO:0046683 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046683 * Deleted definition dbxref ISBN:0721662544 from GO:0046684 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046684 * Deleted definition dbxref ISBN:0721662544 from GO:0046685 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046685 * Deleted definition dbxref ISBN:0721662544 from GO:0046687 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046687 * Deleted definition dbxref ISBN:0721662544 from GO:0046691 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046691 * Deleted definition dbxref ISBN:0721662544 from GO:0046697 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046697 * Deleted definition dbxref ISBN:0721662544 from GO:0046904 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0046904 * Changed synonym scope of GO:0047663 from "Related" to "Exact" * Changed synonym scope of GO:0050405 from "Broad" to "Exact" * Changed definition of GO:0050659 from "Catalysis of the reactions: 3'-phosphoadenylyl sulfate + dermatan = adenosine 3',5'-bisphosphate + dermatan 6'-sulfate.3'-phosphoadenylyl sulfate + chondroitin = adenosine 3',5'-bisphosphate + chondroitin 6'-sulfate." to "Catalysis of the reactions: 3'-phosphoadenylyl sulfate + dermatan = adenosine 3',5'-bisphosphate + dermatan 6'-sulfate and 3'-phosphoadenylyl sulfate + chondroitin = adenosine 3',5'-bisphosphate + chondroitin 6'-sulfate." * Deleted definition dbxref ISBN:0721662544 from GO:0050673 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0050673 * Deleted definition dbxref ISBN:0721662544 from GO:0050674 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0050674 * Deleted definition dbxref ISBN:0721662544 from GO:0050886 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0050886 * Deleted definition dbxref ISBN:0721662544 from GO:0050893 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0050893 * Deleted definition dbxref ISBN:0721662544 from GO:0050894 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0050894 * Deleted definition dbxref ISBN:0721662544 from GO:0050898 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0050898 * Deleted definition dbxref ISBN:0721662544 from GO:0050899 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0050899 * Changed synonym scope of GO:0051007 from "Related" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0051124 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0051124 * Deleted definition dbxref ISBN:0721662544 from GO:0051167 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0051167 * Deleted definition dbxref ISBN:0721662544 from GO:0051337 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0051337 * Deleted definition dbxref ISBN:0721662544 from GO:0051413 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0051413 * Deleted definition dbxref ISBN:0721662544 from GO:0051414 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0051414 * Deleted definition dbxref ISBN:0721662544 from GO:0051501 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0051501 * Deleted definition dbxref ISBN:0721662544 from GO:0051546 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0051546 * Added synonym "DNA demethylase activity" to GO:0051747 * Changed synonym scope of GO:0051747 from "Related" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0051871 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0051871 * Changed synonym scope of GO:0055063 from "Broad" to "Exact" * Deleted definition dbxref ISBN:0721662544 from GO:0060017 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0060017 * Deleted definition dbxref ISBN:0721662544 from GO:0060021 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0060021 * Deleted general dbxref ISBN:0721662544 from synonym palatum development of GO:0060021 * Added general dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to synonym palatum development of GO:0060021 * Deleted definition dbxref ISBN:0721662544 from GO:0060022 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0060022 * Deleted general dbxref ISBN:0721662544 from synonym palatum durum development of GO:0060022 * Added general dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to synonym palatum durum development of GO:0060022 * Deleted definition dbxref ISBN:0721662544 from GO:0060023 * Added definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to GO:0060023 * Deleted general dbxref ISBN:0721662544 from synonym palatum molle development of GO:0060023 * Added general dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to synonym palatum molle development of GO:0060023 * Deleted general dbxref ISBN:0721662544 from synonym velum palatum development of GO:0060023 * Added general dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) to synonym velum palatum development of GO:0060023 * Changed synonym scope of GO:0060126 from "Related" to "Exact" From gocvs at genome.stanford.edu Wed Apr 9 21:30:44 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Wed, 9 Apr 2008 21:30:44 -0700 (PDT) Subject: [Go-diff] GO update 04/09/2008 Message-ID: <200804100430.VAA13634@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.753 by 5.754 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory From gocvs at genome.stanford.edu Thu Apr 10 21:30:46 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Thu, 10 Apr 2008 21:30:46 -0700 (PDT) Subject: [Go-diff] GO update 04/10/2008 Message-ID: <200804110430.VAA23389@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.754 by 5.755 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0043898 * Populated new object GO:0043898 (macro) * Changed name of GO:0043898 from "" to "2,3-dihydroxybiphenyl 1,2-dioxygenase activity" * Set definition of GO:0043898 to "Catalysis of the reaction: 2,3-dihydroxybiphenyl + O2 = 2-hydroxy-6-phenylhexa-2,4-dienoic acid." * Added definition dbxref GOC:jl to GO:0043898 * Added definition dbxref PMID:15715866 to GO:0043898 * Added GO:0043898 to category gosubset_prok * Added synonym "2,3-dihydroxybiphenyl-1,2-dioxygenase activity" to GO:0043898 * Changed synonym scope of GO:0043898 from "Related" to "Exact" * Added synonym "BphC" to GO:0043898 * Copied GO:0043898 to GO:0016702 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0043898 * Removed GO:0000044 from category gosubset_prok * Removed GO:0000067 from category gosubset_prok * Removed GO:0000504 from category gosubset_prok * Removed GO:0003969 from category goslim_pir * Removed GO:0003969 from category gosubset_prok * Removed GO:0005941 from category goslim_generic * Removed GO:0005941 from category goslim_goa * Removed GO:0005941 from category goslim_pir * Removed GO:0005941 from category goslim_plant * Removed GO:0005941 from category gosubset_prok * Removed GO:0006100 from category gosubset_prok * Removed GO:0006118 from category goslim_candida * Removed GO:0006118 from category goslim_generic * Removed GO:0006118 from category goslim_goa * Removed GO:0006118 from category goslim_pir * Removed GO:0006118 from category goslim_plant * Removed GO:0006118 from category goslim_yeast * Removed GO:0006118 from category gosubset_prok * Removed GO:0006125 from category gosubset_prok * Removed GO:0006133 from category gosubset_prok * Removed GO:0006299 from category gosubset_prok * Removed GO:0006484 from category gosubset_prok * Removed GO:0006755 from category gosubset_prok * Removed GO:0009417 from category gosubset_prok * Removed GO:0009502 from category gosubset_prok * Removed GO:0015282 from category gosubset_prok * Removed GO:0015323 from category gosubset_prok * Removed GO:0015428 from category gosubset_prok * Removed GO:0015447 from category gosubset_prok * Removed GO:0015448 from category gosubset_prok * Removed GO:0015449 from category gosubset_prok * Removed GO:0015477 from category gosubset_prok * Added GO:0018571 to category gosubset_prok * Added synonym "2,3-dihydroxy-p-cumate 3,4-dioxygenase" to GO:0018571 * Changed synonym scope of GO:0018571 from "Related" to "Exact" * Added synonym "2,3-dihydroxy-p-cumate-3,4-dioxygenase" to GO:0018571 * Changed synonym scope of GO:0018571 from "Related" to "Exact" * Changed synonym scope of GO:0018583 from "Exact" to "Broad" * Changed synonym scope of GO:0018583 from "Exact" to "Broad" * Removed GO:0033171 from category gosubset_prok * Removed GO:0033236 from category gosubset_prok * Removed GO:0033237 from category gosubset_prok * Removed GO:0045331 from category gosubset_prok * Removed GO:0051843 from category gosubset_prok * Removed GO:0051845 from category gosubset_prok * Removed GO:0051846 from category gosubset_prok * Removed GO:0051853 from category gosubset_prok From gocvs at genome.stanford.edu Fri Apr 11 21:30:46 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Fri, 11 Apr 2008 21:30:46 -0700 (PDT) Subject: [Go-diff] GO update 04/11/2008 Message-ID: <200804120430.VAA03881@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.26 by 1.29 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034397 * Created object of type obo:TERM with id GO:0034398 * Created object of type obo:TERM with id GO:0034399 * Created object of type obo:TERM with id GO:0034400 * Created object of type obo:TERM with id GO:0034401 * Created object of type obo:TERM with id GO:0034402 * Created object of type obo:TERM with id GO:0034403 * Created object of type obo:TERM with id GO:0055115 * Created object of type obo:TERM with id GO:0055116 * Created object of type obo:TERM with id GO:0060232 * Created object of type obo:TERM with id GO:0060233 * Created object of type obo:TERM with id GO:0060234 * Populated new object GO:0034397 (macro) * Changed name of GO:0034397 from "" to "telomere localization" * Set definition of GO:0034397 to "The processes by which a telomere is transported to, and/or maintained in, a specific location." * Added definition dbxref GOC:mah to GO:0034397 * Copied GO:0034397 to GO:0032200 with type OBO_REL:is_a * Copied GO:0034397 to GO:0050000 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034397 * Populated new object GO:0034398 (macro) * Changed name of GO:0034398 from "" to "telomere tethering at nuclear periphery" * Set definition of GO:0034398 to "The process by which a telomere is maintained in a specific location at the nuclear periphery." * Added definition dbxref GOC:mah to GO:0034398 * Copied GO:0034398 to GO:0034397 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034398 * Populated new object GO:0034399 (macro) * Changed name of GO:0034399 from "" to "nuclear periphery" * Set definition of GO:0034399 to "The region of the nucleus adjacent to the nuclear envelope." * Added definition dbxref GOC:krc to GO:0034399 * Copied GO:0034399 to GO:0044428 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034399 * Populated new object GO:0034400 (macro) * Changed name of GO:0034400 from "" to "gerontoplast" * Set definition of GO:0034400 to "A plastid found in senescing, formerly green tissues that is derived from a chloroplast that undergoes an organized developmental program of senescence." * Added definition dbxref PMID:12654863 to GO:0034400 * Added definition dbxref PMID:16151876 to GO:0034400 * Copied GO:0034400 to GO:0009536 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034400 * Populated new object GO:0034401 (macro) * Changed name of GO:0034401 from "" to "establishment and/or maintenance of chromatin architecture during transcription" * Set definition of GO:0034401 to "The specification, formation and maintenance of the physical structure of eukaryotic chromatin during transcription." * Added definition dbxref GOC:curators to GO:0034401 * Copied GO:0034401 to GO:0006325 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034401 * Populated new object GO:0034402 (macro) * Changed name of GO:0034402 from "" to "recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex" * Set definition of GO:0034402 to "The process by which proteins required for 3'-end transcript processing become associated with the RNA polymerase II holoenzyme complex and the 3' end of a transcript." * Added definition dbxref PMID:18195044 to GO:0034402 * Copied GO:0034402 to GO:0031124 with type part_of * Copied GO:0034402 to GO:0022618 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034402 * Populated new object GO:0034403 (macro) * Changed name of GO:0034403 from "" to "alignment of 3' and 5' splice sites of nuclear mRNA" * Set definition of GO:0034403 to "Recognition of both the 5' and 3'-splice sites and positioning them in the correct alignment with respect to each other so that the second catalytic step of nuclear mRNA splicing can occur." * Added definition dbxref GOC:krc to GO:0034403 * Added definition dbxref PMID:9430647 to GO:0034403 * Copied GO:0034403 to GO:0000350 with type part_of * Copied GO:0034403 to GO:0000389 with type OBO_REL:is_a * Copied GO:0034403 to GO:0000395 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034403 * Populated new object GO:0055115 (macro) * Changed name of GO:0055115 from "" to "diapause" * Set definition of GO:0055115 to "A neurohormonally mediated, dynamic state of low metabolic activity. Associated characteristics of this form of dormancy include reduced morphogenesis, increased resistance to environmental extremes, and altered or reduced behavioral activity. Full expression develops in a species-specific manner, usually in response to a number of environmental stimuli that precede unfavorable conditions. Once diapause has begun, metabolic activity is suppressed even if conditions favorable for development prevail. Once initiated, only certain stimuli are capable of releasing the organism from this state, and this characteristic is essential in distinguishing diapause from hibernation." * Added definition dbxref GOC:ds to GO:0055115 * Added definition dbxref GOC:jid to GO:0055115 * Copied GO:0055115 to GO:0022611 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0055115 * Populated new object GO:0055116 (macro) * Changed name of GO:0055116 from "" to "reproductive diapause" * Set definition of GO:0055116 to "A form of diapause where the organism itself will remain fully active, including feeding and other routine activities, but the reproductive organs experience a tissue-specific reduction in metabolism, with characteristic triggering and releasing stimuli." * Added definition dbxref GOC:ds to GO:0055116 * Added definition dbxref GOC:jid to GO:0055116 * Copied GO:0055116 to GO:0055115 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0055116 * Populated new object GO:0060232 (macro) * Changed name of GO:0060232 from "" to "delamination" * Set definition of GO:0060232 to "The negative regulation of cell adhesion process by which a cell or sheet of cells splits off of an existing epithelial sheet." * Added definition dbxref GOC:dph to GO:0060232 * Added definition dbxref PMID:16962574 to GO:0060232 * Added definition dbxref PMID:18343170 to GO:0060232 * Copied GO:0060232 to GO:0022408 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0060232 * Populated new object GO:0060233 (macro) * Changed name of GO:0060233 from "" to "oenocyte delamination" * Set definition of GO:0060233 to "The negative regulation of cell adhesion process by which an oenocyte splits off of an existing epithelial sheet." * Added definition dbxref GOC:dph to GO:0060233 * Copied GO:0060233 to GO:0060232 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0060233 * Populated new object GO:0060234 (macro) * Changed name of GO:0060234 from "" to "neuroblast delamination" * Set definition of GO:0060234 to "The negative regulation of cell adhesion process by which a neuroblast slits off of a neurectodermal sheet." * Added definition dbxref GOC:dph to GO:0060234 * Copied GO:0060234 to GO:0060232 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0060234 * Changed name of GO:0000391 from "U2-dependent spliceosome disassembly" to "U2-type spliceosome disassembly" * Deleted synonym "U2-type spliceosome disassembly" from GO:0000391 * Changed name of GO:0000392 from "U12-dependent spliceosome disassembly" to "U12-type spliceosome disassembly" * Deleted synonym "U12-type spliceosome disassembly" from GO:0000392 * Deleted GO:0000786 --OBO_REL:is_a--> GO:0043234 * Copied GO:0000786 to GO:0032993 with type OBO_REL:is_a * Copied GO:0001837 to GO:0060232 with type OBO_REL:is_a * Copied GO:0002500 to GO:0007039 with type OBO_REL:is_a * Copied GO:0006853 to GO:0032365 with type OBO_REL:is_a * Deleted GO:0007041 --OBO_REL:is_a--> GO:0046907 * Copied GO:0007041 to GO:0007034 with type OBO_REL:is_a * Copied GO:0016456 to GO:0030529 with type OBO_REL:is_a * Copied GO:0019090 to GO:0006839 with type OBO_REL:is_a * Added synonym "metachromatic granule" to GO:0020022 * Added general dbxref PMID:15738951 to synonym metachromatic granule of GO:0020022 * Changed synonym scope of GO:0020022 from "Related" to "Exact" * Added synonym "polyphosphate vacuole" to GO:0020022 * Added general dbxref PMID:15738951 to synonym polyphosphate vacuole of GO:0020022 * Added synonym "volutin granule" to GO:0020022 * Added general dbxref PMID:15738951 to synonym volutin granule of GO:0020022 * Changed synonym scope of GO:0020022 from "Related" to "Exact" * Copied GO:0030033 to GO:0030031 with type OBO_REL:is_a * Deleted GO:0030709 --OBO_REL:is_a--> GO:0022408 * Copied GO:0030709 to GO:0060232 with type OBO_REL:is_a * Deleted GO:0032122 --OBO_REL:is_a--> GO:0006996 * Copied GO:0032122 to GO:0030030 with type OBO_REL:is_a * Deleted GO:0033298 --OBO_REL:is_a--> GO:0006996 * Copied GO:0033298 to GO:0007033 with type OBO_REL:is_a * Changed definition of GO:0042714 from "The aggregation, arrangement and bonding together of proteins on DNA to form the complex that mediates dosage compensation on one or more X chromosomes." to "The aggregation, arrangement and bonding together of proteins on DNA or RNA to form the complex that mediates dosage compensation on one or more X chromosomes." * Deleted GO:0042714 --OBO_REL:is_a--> GO:0065004 * Copied GO:0042714 to GO:0065003 with type OBO_REL:is_a * Copied GO:0043001 to GO:0006886 with type OBO_REL:is_a * Copied GO:0043504 to GO:0032042 with type OBO_REL:is_a * Changed name of GO:0045141 from "telomere clustering" to "meiotic telomere clustering" * Copied GO:0045141 to GO:0034397 with type OBO_REL:is_a * Deleted GO:0046536 --OBO_REL:is_a--> GO:0043234 * Copied GO:0046536 to GO:0044421 with type OBO_REL:is_a * Changed name of GO:0048268 from "clathrin cage assembly" to "clathrin coat assembly" * Changed definition of GO:0048268 from "Assembly of clathrin triskelia into clathrin cage." to "The process by which clathrin triskelia are assembled into the ordered structure known as a clathrin cage." * Deleted synonym "clathrin coat assembly" from GO:0048268 * Added synonym "clathrin cage assembly" to GO:0048268 * Changed synonym scope of GO:0048268 from "Related" to "Exact" * Copied GO:0048268 to GO:0006461 with type OBO_REL:is_a * Deleted GO:0048753 --OBO_REL:is_a--> GO:0006996 * Copied GO:0048753 to GO:0016050 with type OBO_REL:is_a * Added synonym "compartment boundary formation" to GO:0048859 * Added general dbxref GOC:dph to synonym compartment boundary formation of GO:0048859 * Changed synonym scope of GO:0048859 from "Related" to "Narrow" * Deleted GO:0051417 --OBO_REL:is_a--> GO:0007020 * Copied GO:0051417 to GO:0051418 with type OBO_REL:is_a * Deleted GO:0055112 --OBO_REL:is_a--> GO:0022408 * Copied GO:0055112 to GO:0060232 with type OBO_REL:is_a From gocvs at genome.stanford.edu Mon Apr 14 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Mon, 14 Apr 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 04/14/2008 Message-ID: <200804150430.VAA08261@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.29 by 1.32 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0060235 * Populated new object GO:0060235 (macro) * Changed name of GO:0060235 from "" to "lens induction in camera-type eye" * Set definition of GO:0060235 to "Signaling at short range between the head ectoderm and the optic vesicle that results in the head ectoderm forming a lens." * Added definition dbxref GOC:dph to GO:0060235 * Added definition dbxref ISBN:0878932437 to GO:0060235 * Copied GO:0060235 to GO:0002089 with type part_of * Copied GO:0060235 to GO:0031128 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0060235 * Deleted GO:0000335 --OBO_REL:is_a--> GO:0045910 * Deleted GO:0000336 --OBO_REL:is_a--> GO:0045911 * Deleted GO:0002652 --OBO_REL:is_a--> GO:0002819 * Changed definition of GO:0006099 from "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two C02 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." to "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." * Deleted GO:0007096 --OBO_REL:is_a--> GO:0010564 * Changed definition of GO:0007292 from "The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell." to "Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction." * Added definition dbxref GOC:dph to GO:0007292 * Deleted GO:0010503 --OBO_REL:is_a--> GO:0032108 * Deleted GO:0010520 --OBO_REL:is_a--> GO:0010564 * Deleted GO:0019787 --OBO_REL:is_a--> GO:0003824 * Deleted GO:0030071 --OBO_REL:is_a--> GO:0010564 * Deleted GO:0032430 --OBO_REL:is_a--> GO:0060193 * Deleted GO:0032884 --OBO_REL:is_a--> GO:0051128 * Deleted synonym "cyclohexadienyl dehydrogenase activity" from GO:0033731 * Deleted synonym "ribonuclease U2 activity" from GO:0033899 * Deleted GO:0034091 --OBO_REL:is_a--> GO:0010564 * Changed definition of GO:0034400 from "A plastid found in senescing, formerly green tissues that is derived from a chloroplast that undergoes an organized developmental program of senescence." to "A plastid found in senescing, formerly green tissues that is derived from a chloroplast that undergoes an organized developmental program of senescence." * Changed definition of GO:0034403 from "Recognition of both the 5' and 3'-splice sites and positioning them in the correct alignment with respect to each other so that the second catalytic step of nuclear mRNA splicing can occur." to "Recognition of both the 5' and 3'-splice sites and positioning them in the correct alignment with respect to each other so that the second catalytic step of nuclear mRNA splicing can occur." * Deleted GO:0042627 --part_of--> GO:0005615 * Deleted synonym "vitamin B6 metabolic process" from GO:0042818 * Deleted synonym "vitamin B6 metabolism" from GO:0042818 * Deleted GO:0043286 --OBO_REL:is_a--> GO:0009889 * Deleted GO:0043504 --part_of--> GO:0000002 * Deleted GO:0045212 --OBO_REL:is_a--> GO:0009059 * Deleted GO:0045936 --OBO_REL:is_a--> GO:0031324 * Deleted GO:0045937 --OBO_REL:is_a--> GO:0031325 * Deleted GO:0046017 --OBO_REL:is_a--> GO:0022402 * Deleted GO:0046020 --OBO_REL:is_a--> GO:0000122 * Deleted GO:0046021 --OBO_REL:is_a--> GO:0022402 * Deleted GO:0046023 --OBO_REL:is_a--> GO:0022402 * Deleted GO:0046599 --OBO_REL:is_a--> GO:0010564 * Deleted GO:0048135 --part_of--> GO:0007292 * Copied GO:0048135 to GO:0048477 with type part_of * Changed definition of GO:0048232 from "Generation of the male gamete; specialised haploid cells produced by meiosis and involved in sexual reproduction." to "Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction." * Added definition dbxref GOC:dph to GO:0048232 From gocvs at genome.stanford.edu Tue Apr 15 21:30:46 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Tue, 15 Apr 2008 21:30:46 -0700 (PDT) Subject: [Go-diff] GO update 04/15/2008 Message-ID: <200804160430.VAA20488@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.32 by 1.33 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034404 * Populated new object GO:0034404 (macro) * Changed name of GO:0034404 from "" to "nucleobase, nucleoside and nucleotide biosynthetic process" * Set definition of GO:0034404 to "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides and nucleotides." * Added definition dbxref GOC:mah to GO:0034404 * Added synonym "nucleobase, nucleoside and nucleotide anabolism" to GO:0034404 * Changed synonym scope of GO:0034404 from "Related" to "Exact" * Added synonym "nucleobase, nucleoside and nucleotide biosynthesis" to GO:0034404 * Changed synonym scope of GO:0034404 from "Related" to "Exact" * Added synonym "nucleobase, nucleoside and nucleotide formation" to GO:0034404 * Changed synonym scope of GO:0034404 from "Related" to "Exact" * Added synonym "nucleobase, nucleoside and nucleotide synthesis" to GO:0034404 * Changed synonym scope of GO:0034404 from "Related" to "Exact" * Copied GO:0034404 to GO:0055086 with type OBO_REL:is_a * Copied GO:0034404 to GO:0044249 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034404 * Added synonym "MAPK signaling" to GO:0000165 * Added synonym "MAPK signalling" to GO:0000165 * Added synonym "MAPK activation" to GO:0000187 * Changed synonym scope of GO:0000187 from "Related" to "Exact" * Copied GO:0006350 to GO:0043284 with type OBO_REL:is_a * Added synonym "signaling cascade" to GO:0007165 * Changed synonym scope of GO:0007165 from "Related" to "Exact" * Added synonym "signalling cascade" to GO:0007165 * Changed synonym scope of GO:0007165 from "Related" to "Exact" * Copied GO:0009117 to GO:0034404 with type OBO_REL:is_a * Copied GO:0009163 to GO:0034404 with type OBO_REL:is_a * Changed definition of GO:0031214 from "Formation of hard tissues that consist mainly of norganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation." to "Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation." * Added synonym "mineralization" to GO:0031214 * Changed synonym scope of GO:0031214 from "Related" to "Exact" * Deleted definition dbxref PUBMED:15355794 from GO:0042475 * Added definition dbxref PMID:15355794 to GO:0042475 * Deleted definition dbxref PUBMED:15355794 from GO:0042487 * Added definition dbxref PMID:15355794 to GO:0042487 * Deleted definition dbxref PUBMED:15355794 from GO:0042488 * Added definition dbxref PMID:15355794 to GO:0042488 * Deleted definition dbxref PUBMED:15355794 from GO:0042489 * Added definition dbxref PMID:15355794 to GO:0042489 * Copied GO:0046112 to GO:0034404 with type OBO_REL:is_a * Added synonym "NF-kappaB activation" to GO:0051092 * Changed synonym scope of GO:0051092 from "Related" to "Exact" * Added synonym "nucleobase, nucleoside and nucleotide metabolism" to GO:0055086 * Changed synonym scope of GO:0055086 from "Related" to "Exact" From gocvs at genome.stanford.edu Wed Apr 16 21:30:46 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Wed, 16 Apr 2008 21:30:46 -0700 (PDT) Subject: [Go-diff] GO update 04/16/2008 Message-ID: <200804170430.VAA00956@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.33 by 1.37 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034405 * Created object of type obo:TERM with id GO:0055117 * Created object of type obo:TERM with id GO:0055118 * Created object of type obo:TERM with id GO:0055119 * Populated new object GO:0034405 (macro) * Changed name of GO:0034405 from "" to "response to fluid shear stress" * Set definition of GO:0034405 to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface." * Added definition dbxref GOC:sl to GO:0034405 * Copied GO:0034405 to GO:0006950 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034405 * Populated new object GO:0055117 (macro) * Changed name of GO:0055117 from "" to "regulation of cardiac muscle contraction" * Set definition of GO:0055117 to "Any process that modulates the frequency, rate or extent of cardiac muscle contraction." * Added definition dbxref GOC:ed to GO:0055117 * Copied GO:0055117 to GO:0006937 with type OBO_REL:is_a * Copied GO:0055117 to GO:0060048 with type part_of * Assigned namespace "biological_process" to GO:0055117 * Populated new object GO:0055118 (macro) * Changed name of GO:0055118 from "" to "negative regulation of cardiac muscle contraction" * Set definition of GO:0055118 to "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle contraction." * Added definition dbxref GOC:ed to GO:0055118 * Copied GO:0055118 to GO:0045932 with type OBO_REL:is_a * Copied GO:0055118 to GO:0055117 with type OBO_REL:is_a * Copied GO:0055118 to GO:0060048 with type negatively_regulates * Assigned namespace "biological_process" to GO:0055118 * Populated new object GO:0055119 (macro) * Changed name of GO:0055119 from "" to "relaxation of cardiac muscle" * Set definition of GO:0055119 to "The process whereby the extent of cardiac muscle contraction is reduced." * Added definition dbxref GOC:ed to GO:0055119 * Copied GO:0055119 to GO:0055118 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0055119 * Deleted GO:0000384 --OBO_REL:is_a--> GO:0000385 * Copied GO:0000384 to GO:0031202 with type OBO_REL:is_a * Deleted GO:0000385 --OBO_REL:is_a--> GO:0003824 * Deleted GO:0000384 --OBO_REL:is_a--> GO:0000385 * Deleted GO:0000386 --OBO_REL:is_a--> GO:0000385 * Destroyed object GO:0000385 * Deleted GO:0000386 --OBO_REL:is_a--> GO:0000385 * Copied GO:0000386 to GO:0031202 with type OBO_REL:is_a * Deleted synonym "AATK" from GO:0004714 * Deleted synonym "AATYK" from GO:0004714 * Deleted synonym "AATYK2" from GO:0004714 * Deleted synonym "AATYK3" from GO:0004714 * Deleted synonym "ACH" from GO:0004714 * Deleted synonym "ALK" from GO:0004714 * Deleted synonym "ARK" from GO:0004714 * Deleted synonym "AXL" from GO:0004714 * Deleted synonym "Bek" from GO:0004714 * Deleted synonym "bfgfr" from GO:0004714 * Deleted synonym "BRT" from GO:0004714 * Deleted synonym "Bsk" from GO:0004714 * Deleted synonym "C-FMS" from GO:0004714 * Deleted synonym "CAK" from GO:0004714 * Deleted synonym "CCK4" from GO:0004714 * Deleted synonym "CD115" from GO:0004714 * Deleted synonym "CD135" from GO:0004714 * Deleted synonym "CDw135" from GO:0004714 * Deleted synonym "Cek1" from GO:0004714 * Deleted synonym "Cek10" from GO:0004714 * Deleted synonym "Cek11" from GO:0004714 * Deleted synonym "Cek2" from GO:0004714 * Deleted synonym "Cek3" from GO:0004714 * Deleted synonym "Cek5" from GO:0004714 * Deleted synonym "Cek6" from GO:0004714 * Deleted synonym "Cek7" from GO:0004714 * Deleted synonym "CFD1" from GO:0004714 * Deleted synonym "CKIT" from GO:0004714 * Deleted synonym "CSF1R" from GO:0004714 * Deleted synonym "DAlk" from GO:0004714 * Deleted synonym "DDR1" from GO:0004714 * Deleted synonym "DDR2" from GO:0004714 * Deleted synonym "Dek" from GO:0004714 * Deleted synonym "DKFZp434C1418" from GO:0004714 * Deleted synonym "DRT" from GO:0004714 * Deleted synonym "DTK" from GO:0004714 * Deleted synonym "Ebk" from GO:0004714 * Deleted synonym "ECK" from GO:0004714 * Deleted synonym "EDDR1" from GO:0004714 * Deleted synonym "Eek" from GO:0004714 * Deleted synonym "EGFR" from GO:0004714 * Deleted synonym "Ehk2" from GO:0004714 * Deleted synonym "Ehk3" from GO:0004714 * Deleted synonym "Elk" from GO:0004714 * Deleted synonym "EPH" from GO:0004714 * Deleted synonym "EPHA1" from GO:0004714 * Deleted synonym "EPHA2" from GO:0004714 * Deleted synonym "EPHA6" from GO:0004714 * Deleted synonym "EPHA7" from GO:0004714 * Deleted synonym "EPHA8" from GO:0004714 * Deleted synonym "EPHB1" from GO:0004714 * Deleted synonym "EPHB2" from GO:0004714 * Deleted synonym "EPHB3" from GO:0004714 * Deleted synonym "EPHB4" from GO:0004714 * Deleted synonym "EphB5" from GO:0004714 * Deleted synonym "EPHT" from GO:0004714 * Deleted synonym "EPHT2" from GO:0004714 * Deleted synonym "EPHT3" from GO:0004714 * Deleted synonym "EPHX" from GO:0004714 * Deleted synonym "ERBB" from GO:0004714 * Deleted synonym "ERBB1" from GO:0004714 * Deleted synonym "ERBB2" from GO:0004714 * Deleted synonym "ERBB3" from GO:0004714 * Deleted synonym "ERBB4" from GO:0004714 * Deleted synonym "ERK" from GO:0004714 * Deleted synonym "Eyk" from GO:0004714 * Deleted synonym "FGFR1" from GO:0004714 * Deleted synonym "FGFR2" from GO:0004714 * Deleted synonym "FGFR3" from GO:0004714 * Deleted synonym "FGFR4" from GO:0004714 * Deleted synonym "FLG" from GO:0004714 * Deleted synonym "FLK1" from GO:0004714 * Deleted synonym "FLK2" from GO:0004714 * Deleted synonym "FLT1" from GO:0004714 * Deleted synonym "FLT2" from GO:0004714 * Deleted synonym "FLT3" from GO:0004714 * Deleted synonym "FLT4" from GO:0004714 * Deleted synonym "FMS" from GO:0004714 * Deleted synonym "Fv2" from GO:0004714 * Deleted synonym "HBGFR" from GO:0004714 * Deleted synonym "HEK11" from GO:0004714 * Deleted synonym "HEK2" from GO:0004714 * Deleted synonym "HEK3" from GO:0004714 * Deleted synonym "HEK5" from GO:0004714 * Deleted synonym "HEK6" from GO:0004714 * Deleted synonym "HEP" from GO:0004714 * Deleted synonym "HER2" from GO:0004714 * Deleted synonym "HER3" from GO:0004714 * Deleted synonym "HER4" from GO:0004714 * Deleted synonym "HGFR" from GO:0004714 * Deleted synonym "HSCR1" from GO:0004714 * Deleted synonym "HTK" from GO:0004714 * Deleted synonym "IGF1R" from GO:0004714 * Deleted synonym "INSR" from GO:0004714 * Deleted synonym "INSRR" from GO:0004714 * Deleted synonym "IR" from GO:0004714 * Deleted synonym "IRR" from GO:0004714 * Deleted synonym "JTK12" from GO:0004714 * Deleted synonym "JTK13" from GO:0004714 * Deleted synonym "JTK14" from GO:0004714 * Deleted synonym "JWS" from GO:0004714 * Deleted synonym "K-SAM" from GO:0004714 * Deleted synonym "KDR" from GO:0004714 * Deleted synonym "KGFR" from GO:0004714 * Deleted synonym "KIA0641" from GO:0004714 * Deleted synonym "KIAA1079" from GO:0004714 * Deleted synonym "KIAA1459" from GO:0004714 * Deleted synonym "Kil" from GO:0004714 * Deleted synonym "Kin15" from GO:0004714 * Deleted synonym "Kin16" from GO:0004714 * Deleted synonym "KIT" from GO:0004714 * Deleted synonym "KLG" from GO:0004714 * Deleted synonym "LTK" from GO:0004714 * Deleted synonym "MCF3" from GO:0004714 * Deleted synonym "Mdk1" from GO:0004714 * Deleted synonym "Mdk2" from GO:0004714 * Deleted synonym "Mdk5" from GO:0004714 * Deleted synonym "MEhk1" from GO:0004714 * Deleted synonym "MEN2A/B" from GO:0004714 * Deleted synonym "Mep" from GO:0004714 * Deleted synonym "MER" from GO:0004714 * Deleted synonym "MERTK" from GO:0004714 * Deleted synonym "MET" from GO:0004714 * Deleted synonym "Mlk1" from GO:0004714 * Deleted synonym "Mlk2" from GO:0004714 * Deleted synonym "Mrk" from GO:0004714 * Deleted synonym "MST1R" from GO:0004714 * Deleted synonym "MTC1" from GO:0004714 * Deleted synonym "MUSK" from GO:0004714 * Deleted synonym "Myk1" from GO:0004714 * Deleted synonym "N-SAM" from GO:0004714 * Deleted synonym "NEP" from GO:0004714 * Deleted synonym "NET" from GO:0004714 * Deleted synonym "Neu" from GO:0004714 * Deleted synonym "NGL" from GO:0004714 * Deleted synonym "NOK" from GO:0004714 * Deleted synonym "nork" from GO:0004714 * Deleted synonym "Nsk2" from GO:0004714 * Deleted synonym "NTRK1" from GO:0004714 * Deleted synonym "NTRK2" from GO:0004714 * Deleted synonym "NTRK3" from GO:0004714 * Deleted synonym "NTRK4" from GO:0004714 * Deleted synonym "NTRKR1" from GO:0004714 * Deleted synonym "NTRKR2" from GO:0004714 * Deleted synonym "NTRKR3" from GO:0004714 * Deleted synonym "Nuk" from GO:0004714 * Deleted synonym "NYK" from GO:0004714 * Deleted synonym "PCL" from GO:0004714 * Deleted synonym "PDGFR" from GO:0004714 * Deleted synonym "PDGFRA" from GO:0004714 * Deleted synonym "PDGFRB" from GO:0004714 * Deleted synonym "PHB6" from GO:0004714 * Deleted synonym "PTK" from GO:0004714 * Deleted synonym "PTK3" from GO:0004714 * Deleted synonym "PTK7" from GO:0004714 * Deleted synonym "RET" from GO:0004714 * Deleted synonym "RON" from GO:0004714 * Deleted synonym "ROR1" from GO:0004714 * Deleted synonym "ROR2" from GO:0004714 * Deleted synonym "ROS1" from GO:0004714 * Deleted synonym "RSE" from GO:0004714 * Deleted synonym "RTK" from GO:0004714 * Deleted synonym "RYK" from GO:0004714 * Deleted synonym "SEA" from GO:0004714 * Deleted synonym "Sek2" from GO:0004714 * Deleted synonym "Sek3" from GO:0004714 * Deleted synonym "Sek4" from GO:0004714 * Deleted synonym "Sfr" from GO:0004714 * Deleted synonym "SKY" from GO:0004714 * Deleted synonym "STK" from GO:0004714 * Deleted synonym "STK1" from GO:0004714 * Deleted synonym "TEK" from GO:0004714 * Deleted synonym "TIE" from GO:0004714 * Deleted synonym "TIE1" from GO:0004714 * Deleted synonym "TIE2" from GO:0004714 * Deleted synonym "TIF" from GO:0004714 * Deleted synonym "TKT" from GO:0004714 * Deleted synonym "TRK" from GO:0004714 * Deleted synonym "TRKA" from GO:0004714 * Deleted synonym "TRKB" from GO:0004714 * Deleted synonym "TRKC" from GO:0004714 * Deleted synonym "TRKE" from GO:0004714 * Deleted synonym "TYK1" from GO:0004714 * Deleted synonym "TYRO10" from GO:0004714 * Deleted synonym "tyro11" from GO:0004714 * Deleted synonym "TYRO3" from GO:00047