[Go-diff] GO update 05/06/2009
Remote CVS for Gene Ontology
gocvs at genome.stanford.edu
Wed May 6 21:30:54 PDT 2009
OBODIFF of gene_ontology_write.obo version 1.589 by 1.595
Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0002139
* Created object of type obo:TERM with id GO:0002140
* Created object of type obo:TERM with id GO:0002141
* Created object of type obo:TERM with id GO:0002142
* Created object of type obo:TERM with id GO:0002143
* Created object of type obo:TERM with id GO:0010956
* Created object of type obo:TERM with id GO:0010957
* Created object of type obo:TERM with id GO:0010958
* Created object of type obo:TERM with id GO:0010959
* Created object of type obo:TERM with id GO:0010960
* Created object of type obo:TERM with id GO:0010961
* Created object of type obo:TERM with id GO:0060574
* Created object of type obo:TERM with id GO:0060575
* Created object of type obo:TERM with id GO:0060576
* Created object of type obo:TERM with id GO:0060577
* Created object of type obo:TERM with id GO:0060578
* Created object of type obo:TERM with id GO:0070631
* Created object of type obo:TERM with id GO:0070632
* Created object of type obo:TERM with id GO:0070633
* Created object of type obo:TERM with id GO:0070634
* Created object of type obo:TERM with id GO:0080132
* Created object of type obo:TERM with id GO:0080133
* Created object of type obo:TERM with id GO:0080134
* Created object of type obo:TERM with id GO:0080135
* Created object of type obo:TERM with id GO:0080136
* Populated new object GO:0002139 (macro)
* Changed name of GO:0002139 from "<new term>" to "stereocilia coupling link"
* Set definition of GO:0002139 to "A structure involved in coupling stereocilia to one another in sensory hair cells There are 4 morphologically distinct types:tip links, horizontal top connectors, shaft connectors and ankle links. Tip links and horizontal top connectors are the only inter-stereocilia links associated with mature cochlea, whereas ankle links appear during development of the auditory hair bundle."
* Added definition dbxref PMID:16775142 to GO:0002139
* Copied GO:0002139 to GO:0044464 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0002139
* Populated new object GO:0002140 (macro)
* Changed name of GO:0002140 from "<new term>" to "stereocilia tip link"
* Set definition of GO:0002140 to "A stereocilia link that is formed by a fine filament running more or less vertically upward from the tip of each shorter stereocilium to attach at a higher point on its adjacent taller neighbor. Tilting the bundle puts tension on the filaments, which pull on mechanically gated ion channels in the membrane of the stereocilia."
* Added definition dbxref PMID:1108787 to GO:0002140
* Copied GO:0002140 to GO:0002139 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0002140
* Populated new object GO:0002141 (macro)
* Changed name of GO:0002141 from "<new term>" to "stereocilia ankle link"
* Set definition of GO:0002141 to "A stereocilia coupling link that is composed of a fine filament present in developing stereocilia that couples the bases of individual stereocilia to one another. They are not present in mature stereocilia."
* Added definition dbxref PMID:17567809 to GO:0002141
* Copied GO:0002141 to GO:0002139 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0002141
* Populated new object GO:0002142 (macro)
* Changed name of GO:0002142 from "<new term>" to "stereocilia ankle link complex"
* Set definition of GO:0002142 to "A complex of proteins that connect growing stereocilia in developing cochlear hair cells, composed of Vlgr1, usherin, vezatin, and whirlin."
* Added definition dbxref PMID:16775142 to GO:0002142
* Copied GO:0002142 to GO:0043234 with type OBO_REL:is_a
* Copied GO:0002142 to GO:0002141 with type part_of
* Assigned namespace "cellular_component" to GO:0002142
* Populated new object GO:0002143 (macro)
* Changed name of GO:0002143 from "<new term>" to "wobble position uridine thiolation"
* Added comment "In E. coli, the first step of the reaction is reductive elimination of sulphur from L-cysteine by IscS cysteine desulphurase to form an enzyme-bound cysteine-persulphide intermediate. Then, five essential gene products, TusA, TusB, TusC, TusD and TusE, mediate a sulphur relay that delivers the terminal sulphur of persulphide from IscS to MnmA12. The last protein, MnmA catalyzes the transfer of the sulfur from IscS to an ATP activated U34 of the tRNA."
* Set definition of GO:0002143 to "The process whereby a uridine residue at position 34 in the anticodon of a tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps."
* Added definition dbxref PMID:16871210 to GO:0002143
* Added synonym "wobble position s2U biosynthesis" to GO:0002143
* Changed synonym scope of GO:0002143 from "Related" to "Exact"
* Copied GO:0002143 to GO:0002098 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0002143
* Populated new object GO:0010956 (macro)
* Changed name of GO:0010956 from "<new term>" to "negative regulation of calcidiol 1-monooxygenase activity"
* Set definition of GO:0010956 to "Any process that decreases the rate, frequency or extent of calcidiol 1-monooxygenase activity. Calcidiol 1-monooxygenase activity is the catalysis of the reaction: calcidiol + NADPH + H+ + O2 = calcitriol + NADP+ + H2O."
* Added definition dbxref GOC:dph to GO:0010956
* Added definition dbxref GOC:tb to GO:0010956
* Copied GO:0010956 to GO:0004498 with type negatively_regulates
* Copied GO:0010956 to GO:0032769 with type OBO_REL:is_a
* Copied GO:0010956 to GO:0060558 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010956
* Populated new object GO:0010957 (macro)
* Changed name of GO:0010957 from "<new term>" to "negative regulation of vitamin D biosynthetic process"
* Set definition of GO:0010957 to "Any process that decreases the rate, frequency or extent of a vitamin D biosynthetic process. Vitamin D biosynthesis is the chemical reactions and pathways resulting in the formation of vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3)."
* Added definition dbxref GOC:dph to GO:0010957
* Added definition dbxref GOC:tb to GO:0010957
* Copied GO:0010957 to GO:0046137 with type OBO_REL:is_a
* Copied GO:0010957 to GO:0042368 with type negatively_regulates
* Copied GO:0010957 to GO:0060556 with type OBO_REL:is_a
* Copied GO:0010957 to GO:0031327 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010957
* Populated new object GO:0010958 (macro)
* Changed name of GO:0010958 from "<new term>" to "regulation of amino acid import"
* Set definition of GO:0010958 to "Any process that modulates the frequency, rate or extent of amino acid import. Amino acid import is the directed movement of amino acids into a cell or organelle."
* Added definition dbxref GOC:dph to GO:0010958
* Added definition dbxref GOC:tb to GO:0010958
* Copied GO:0010958 to GO:0051955 with type OBO_REL:is_a
* Copied GO:0010958 to GO:0043090 with type regulates
* Copied GO:0010958 to GO:0034762 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010958
* Populated new object GO:0010959 (macro)
* Changed name of GO:0010959 from "<new term>" to "regulation of metal ion transport"
* Set definition of GO:0010959 to "Any process that modulates the frequency, rate, or extent of metal ion transport. Metal ion transport is the directed movement of metal ions, any metal ion with an electric charge, into, out of, within or between cells."
* Added definition dbxref GOC:dph to GO:0010959
* Added definition dbxref GOC:tb to GO:0010959
* Copied GO:0010959 to GO:0030001 with type regulates
* Copied GO:0010959 to GO:0043269 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010959
* Populated new object GO:0010960 (macro)
* Changed name of GO:0010960 from "<new term>" to "magnesium ion homeostasis"
* Set definition of GO:0010960 to "Any process involved in the maintenance of an internal equilibrium of magnesium ions within an organism or cell."
* Added definition dbxref GOC:dph to GO:0010960
* Added definition dbxref GOC:tb to GO:0010960
* Copied GO:0010960 to GO:0055065 with type OBO_REL:is_a
* Copied GO:0010960 to GO:0055066 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010960
* Populated new object GO:0010961 (macro)
* Changed name of GO:0010961 from "<new term>" to "cellular magnesium ion homeostasis"
* Set definition of GO:0010961 to "Any process involved in the maintenance of an internal equilibrium of calcium ions at the level of a cell."
* Added definition dbxref GOC:dph to GO:0010961
* Added definition dbxref GOC:tb to GO:0010961
* Copied GO:0010961 to GO:0006875 with type OBO_REL:is_a
* Copied GO:0010961 to GO:0030005 with type OBO_REL:is_a
* Copied GO:0010961 to GO:0010960 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010961
* Populated new object GO:0060574 (macro)
* Changed name of GO:0060574 from "<new term>" to "intestinal epithelial cell maturation"
* Set definition of GO:0060574 to "The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell of the intestine to attain its fully functional state. A columnar/cuboidal epithelial cell of the intestine mature as they migrate from the intestinal crypt to the villus."
* Added definition dbxref GOC:dph to GO:0060574
* Added definition dbxref PMID:18824147 to GO:0060574
* Copied GO:0060574 to GO:0060576 with type part_of
* Copied GO:0060574 to GO:0002069 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0060574
* Populated new object GO:0060575 (macro)
* Changed name of GO:0060575 from "<new term>" to "intestinal epithelial cell differentiation"
* Set definition of GO:0060575 to "The process whereby a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell of the intestine."
* Added definition dbxref GOC:dph to GO:0060575
* Copied GO:0060575 to GO:0002065 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0060575
* Populated new object GO:0060576 (macro)
* Changed name of GO:0060576 from "<new term>" to "intestinal epithelial cell development"
* Set definition of GO:0060576 to "The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure."
* Added definition dbxref GOC:dph to GO:0060576
* Copied GO:0060576 to GO:0002066 with type OBO_REL:is_a
* Copied GO:0060576 to GO:0060575 with type part_of
* Assigned namespace "biological_process" to GO:0060576
* Populated new object GO:0060577 (macro)
* Changed name of GO:0060577 from "<new term>" to "pulmonary vein morphogenesis"
* Set definition of GO:0060577 to "The process by which the anatomical structure of the pulmonary venous blood vessels are generated and organized. Pulmonary veins are blood vessels that transport blood from the lungs to the heart."
* Added definition dbxref GOC:dph to GO:0060577
* Added synonym "pulmonary venous blood vessel morphogenesis" to GO:0060577
* Added general dbxref GOC:dph to synonym pulmonary venous blood vessel morphogenesis of GO:0060577
* Copied GO:0060577 to GO:0048845 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0060577
* Populated new object GO:0060578 (macro)
* Changed name of GO:0060578 from "<new term>" to "superior vena cava morphogenesis"
* Set definition of GO:0060578 to "The process by which the anatomical structure of superior vena cava generated and organized. The superior vena cava is a blood vessel that transports blood from the upper body to the heart."
* Added definition dbxref GOC:dph to GO:0060578
* Copied GO:0060578 to GO:0048845 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0060578
* Populated new object GO:0070631 (macro)
* Changed name of GO:0070631 from "<new term>" to "spindle pole body localization"
* Set definition of GO:0070631 to "Any process by which a spindle pole body is transported to, or maintained in, a specific location. A spindle pole body is a type of microtubule organizing center found in fungal cells."
* Added definition dbxref GOC:mah to GO:0070631
* Added synonym "establishment and maintenance of spindle pole body localization" to GO:0070631
* Added general dbxref GOC:mah to synonym establishment and maintenance of spindle pole body localization of GO:0070631
* Changed synonym scope of GO:0070631 from "Related" to "Exact"
* Copied GO:0070631 to GO:0051641 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070631
* Populated new object GO:0070632 (macro)
* Changed name of GO:0070632 from "<new term>" to "establishment of spindle pole body localization"
* Set definition of GO:0070632 to "Any process by which a spindle pole body is transported to a specific location. A spindle pole body is a type of microtubule organizing center found in fungal cells."
* Added definition dbxref GOC:mah to GO:0070632
* Added synonym "spindle pole body positioning" to GO:0070632
* Added general dbxref GOC:vw to synonym spindle pole body positioning of GO:0070632
* Changed synonym scope of GO:0070632 from "Related" to "Exact"
* Copied GO:0070632 to GO:0070631 with type OBO_REL:is_a
* Copied GO:0070632 to GO:0051649 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070632
* Populated new object GO:0070633 (macro)
* Changed name of GO:0070633 from "<new term>" to "transepithelial transport"
* Set definition of GO:0070633 to "The directed movement of a substance from one side of an epithelium to the other."
* Added definition dbxref GOC:mah to GO:0070633
* Added definition dbxref ISBN:0716731363 to GO:0070633
* Copied GO:0070633 to GO:0006810 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070633
* Populated new object GO:0070634 (macro)
* Changed name of GO:0070634 from "<new term>" to "transepithelial ammonium transport"
* Set definition of GO:0070634 to "The directed movement of ammonium ions from one side of an epithelium to the other."
* Added definition dbxref GOC:mah to GO:0070634
* Added definition dbxref GOC:yaf to GO:0070634
* Copied GO:0070634 to GO:0070633 with type OBO_REL:is_a
* Copied GO:0070634 to GO:0015696 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070634
* Populated new object GO:0080132 (macro)
* Changed name of GO:0080132 from "<new term>" to "fatty acid alpha-hydroxylase activity"
* Set definition of GO:0080132 to "Catalysis of the conversion of a fatty acid to an alpha-hydroxylated fatty acid. A hydroxyl group is added to the second carbon, counted from the carboxyl end, of a fatty acid chain."
* Added definition dbxref PMID:19054355 to GO:0080132
* Added synonym "fatty acid 2-hydroxylase" to GO:0080132
* Changed synonym scope of GO:0080132 from "Related" to "Exact"
* Copied GO:0080132 to GO:0016491 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0080132
* Populated new object GO:0080133 (macro)
* Changed name of GO:0080133 from "<new term>" to "midchain alkane hydroxylase activity"
* Set definition of GO:0080133 to "Catalysis of the conversion of an alkane to a secondary alcohol."
* Added definition dbxref PMID:17905869 to GO:0080133
* Copied GO:0080133 to GO:0016713 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0080133
* Populated new object GO:0080134 (macro)
* Changed name of GO:0080134 from "<new term>" to "regulation of response to stress"
* Set definition of GO:0080134 to "Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)."
* Added definition dbxref GOC:DHL to GO:0080134
* Copied GO:0080134 to GO:0048583 with type OBO_REL:is_a
* Copied GO:0080134 to GO:0006950 with type regulates
* Assigned namespace "biological_process" to GO:0080134
* Populated new object GO:0080135 (macro)
* Changed name of GO:0080135 from "<new term>" to "regulation of cellular response to stress"
* Set definition of GO:0080135 to "Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)."
* Added definition dbxref GOC:DHL to GO:0080135
* Copied GO:0080135 to GO:0080134 with type OBO_REL:is_a
* Copied GO:0080135 to GO:0033554 with type regulates
* Assigned namespace "biological_process" to GO:0080135
* Populated new object GO:0080136 (macro)
* Changed name of GO:0080136 from "<new term>" to "priming of cellular response to stress"
* Set definition of GO:0080136 to "The process that enables cells to respond in a more rapid and robust manner than nonprimed cells to much lower levels of a stimulus indicating the organism is under stress."
* Added definition dbxref PMID:19318610 to GO:0080136
* Added synonym "priming of response to stress" to GO:0080136
* Changed synonym scope of GO:0080136 from "Related" to "Broad"
* Added synonym "priming of stress response" to GO:0080136
* Changed synonym scope of GO:0080136 from "Related" to "Broad"
* Copied GO:0080136 to GO:0080135 with type OBO_REL:is_a
* Copied GO:0080136 to GO:0033554 with type part_of
* Assigned namespace "biological_process" to GO:0080136
* Copied GO:0002542 to GO:0002673 with type OBO_REL:is_a
* Deleted GO:0006038 --OBO_REL:is_a--> GO:0044038
* Deleted GO:0006109 --OBO_REL:is_a--> GO:0019222
* Copied GO:0007090 to GO:0010564 with type OBO_REL:is_a
* Copied GO:0007092 to GO:0032434 with type OBO_REL:is_a
* Deleted GO:0007374 --OBO_REL:is_a--> GO:0009653
* Copied GO:0007374 to GO:0060571 with type OBO_REL:is_a
* Deleted GO:0007531 --part_of--> GO:0048468
* Copied GO:0007531 to GO:0030154 with type OBO_REL:is_a
* Deleted GO:0008895 --OBO_REL:is_a--> GO:0015035
* Destroyed object GO:0008895
* Copied GO:0010635 to GO:0022603 with type OBO_REL:is_a
* Deleted GO:0010697 --OBO_REL:is_a--> GO:0048523
* Deleted GO:0010755 --OBO_REL:is_a--> GO:0031399
* Deleted GO:0010946 --OBO_REL:is_a--> GO:0010564
* Copied GO:0010949 to GO:0060457 with type OBO_REL:is_a
* added secondary id GO:0008895 to GO:0015035
* Deleted definition dbxref MetaCyc:DISULFOXRED-RXN- from GO:0015035
* Added definition dbxref MetaCyc:DISULFOXRED-RXN to GO:0015035
* Added synonym "haem lyase disulphide oxidoreductase activity" to GO:0015035
* Changed synonym scope of GO:0015035 from "Related" to "Narrow"
* Added synonym "heme lyase disulfide oxidoreductase activity" to GO:0015035
* Changed synonym scope of GO:0015035 from "Related" to "Narrow"
* Deleted GO:0015904 --OBO_REL:is_a--> GO:0015893
* Copied GO:0016430 to GO:0008170 with type OBO_REL:is_a
* Deleted GO:0021503 --OBO_REL:is_a--> GO:0009653
* Copied GO:0021503 to GO:0060571 with type OBO_REL:is_a
* Deleted GO:0021505 --OBO_REL:is_a--> GO:0009653
* Copied GO:0021505 to GO:0060571 with type OBO_REL:is_a
* Deleted GO:0021506 --OBO_REL:is_a--> GO:0009653
* Copied GO:0021506 to GO:0002009 with type OBO_REL:is_a
* Deleted GO:0021507 --OBO_REL:is_a--> GO:0009653
* Copied GO:0021507 to GO:0002009 with type OBO_REL:is_a
* Deleted GO:0021993 --OBO_REL:is_a--> GO:0009653
* Copied GO:0021993 to GO:0002009 with type OBO_REL:is_a
* Deleted GO:0021994 --OBO_REL:is_a--> GO:0009653
* Copied GO:0021994 to GO:0002009 with type OBO_REL:is_a
* Deleted GO:0021995 --OBO_REL:is_a--> GO:0009653
* Copied GO:0021995 to GO:0002009 with type OBO_REL:is_a
* Changed definition of GO:0030321 from "The directed movement of chloride ions across an epithelium." to "The directed movement of chloride ions from one side of an epithelium to the other."
* Copied GO:0030321 to GO:0070633 with type OBO_REL:is_a
* Deleted GO:0034221 --part_of--> GO:0009272
* Deleted GO:0043280 --OBO_REL:is_a--> GO:0051345
* Changed name of GO:0045167 from "asymmetric protein localization during cell fate commitment" to "asymmetric protein localization involved in cell fate determination"
* Deleted GO:0045167 --part_of--> GO:0045165
* Copied GO:0045167 to GO:0001709 with type part_of
* Changed name of GO:0045168 from "cell-cell signaling involved in cell fate commitment" to "cell-cell signaling involved in cell fate specification"
* Deleted GO:0045168 --part_of--> GO:0045165
* Copied GO:0045168 to GO:0001708 with type part_of
* Deleted GO:0045835 --OBO_REL:is_a--> GO:0048523
* Changed name of GO:0060520 from "androgen receptor signaling pathway involved in prostate field specification" to "activation of prostate induction by androgen receptor signaling pathway"
* Changed definition of GO:0060520 from "Any series of molecular signals generated as a consequence of an androgen binding to its receptor in the urogenital sinus mesenchyme initiating the release of signals from the mesenchyme that will cause prostatic bud formation." to "Any series of molecular signals generated as a consequence of an androgen binding to its receptor in The process by which any series of molecular signals generated as a consequence of an androgen binding to its receptor in the urogenital sinus mesenchyme initiates prostate induction. Prostate induction is the close range interaction of the urogenital sinus mesenchyme and the urogenital sinus epithelium that causes the cells of the urogenital sinus epithelium to change their fates and specify the development of the prostate gland."
* Added definition dbxref GOC:tb to GO:0060520
* Copied GO:0060520 to GO:0010453 with type OBO_REL:is_a
* Copied GO:0060520 to GO:0010647 with type OBO_REL:is_a
* Copied GO:0060564 to GO:0032435 with type OBO_REL:is_a
* Copied GO:0060569 to GO:0051247 with type OBO_REL:is_a
* Copied GO:0060570 to GO:0051248 with type OBO_REL:is_a
* Copied GO:0070587 to GO:0010470 with type OBO_REL:is_a
* Copied GO:0070608 to GO:0044087 with type OBO_REL:is_a
* Copied GO:0070613 to GO:0010468 with type OBO_REL:is_a
* Copied GO:0070616 to GO:0031326 with type OBO_REL:is_a
* Copied GO:0070617 to GO:0031327 with type OBO_REL:is_a
* Copied GO:0070623 to GO:0031326 with type OBO_REL:is_a
* Copied GO:0070624 to GO:0031327 with type OBO_REL:is_a
* Copied GO:0080092 to GO:0051239 with type OBO_REL:is_a
* Copied GO:0080092 to GO:0043900 with type OBO_REL:is_a
* Copied GO:0080092 to GO:0060284 with type OBO_REL:is_a
* Copied GO:0080092 to GO:0048638 with type OBO_REL:is_a
* Copied GO:0080092 to GO:0051510 with type OBO_REL:is_a
* Copied GO:0080113 to GO:0080050 with type OBO_REL:is_a
* Deleted GO:0080120 --OBO_REL:is_a--> GO:0016485
More information about the Go-diff
mailing list