[Go-diff] GO update 05/19/2009

Tue May 19 21:30:53 PDT 2009

OBODIFF of gene_ontology_write.obo version 1.615 by 1.618

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0060637
* Created object of type obo:TERM with id GO:0060638
* Created object of type obo:TERM with id GO:0080137
* Created object of type obo:TERM with id GO:0080138
* Created object of type obo:TERM with id GO:0080139
* Created object of type obo:TERM with id GO:0080140
* Created object of type obo:TERM with id GO:0080141
* Created object of type obo:TERM with id GO:0080142
* Populated new object GO:0060637 (macro)
  * Changed name of GO:0060637 from "<new term>" to "positive regulation of lactation by mesenchymal-epithelial cell signaling"
  * Set definition of GO:0060637 to "The process that increases the rate, frequency, or extent of lactation as a result of the secretion of a signal from the mammary fat and its reception by a mammary epithelial cell."
  * Added definition dbxref GOC:dph to GO:0060637
  * Added definition dbxref PMID:12558599 to GO:0060637
  * Copied GO:0060637 to GO:0051094 with type OBO_REL:is_a
  * Copied GO:0060637 to GO:0007595 with type positively_regulates
  * Copied GO:0060637 to GO:0051240 with type OBO_REL:is_a
  * Copied GO:0060637 to GO:0060638 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060637
* Populated new object GO:0060638 (macro)
  * Changed name of GO:0060638 from "<new term>" to "mesenchymal-epithelial cell signaling"
  * Set definition of GO:0060638 to "Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell."
  * Added definition dbxref GOC:dph to GO:0060638
  * Copied GO:0060638 to GO:0007267 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060638
* Populated new object GO:0080137 (macro)
  * Changed name of GO:0080137 from "<new term>" to "DNA-directed RNA polymerase V complex"
  * Set definition of GO:0080137 to "RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants. In addition to RNA polymerases I, II, and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, Pol IV and Pol V, that play nonredundant roles in siRNA-directed DNA methylation and gene silencing. Pol IV is required for siRNA production and Pol V is required for generating noncoding transcripts at target loci. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol V are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases."
  * Added definition dbxref PMID:19110459 to GO:0080137
  * Copied GO:0080137 to GO:0055029 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0080137
* Populated new object GO:0080138 (macro)
  * Changed name of GO:0080138 from "<new term>" to "boron uptake transmembrane transporter activity"
  * Set definition of GO:0080138 to "Catalysis of the transfer of boron from the outside of a cell to the inside of the cell across a membrane."
  * Added definition dbxref PMID:18603465 to GO:0080138
  * Copied GO:0080138 to GO:0015563 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080138
* Populated new object GO:0080139 (macro)
  * Changed name of GO:0080139 from "<new term>" to "boron efflux transmembrane transporter activity"
  * Set definition of GO:0080139 to "Catalysis of the transfer of boron from the inside of the cell to the outside of the cell across a membrane."
  * Added definition dbxref PMID:18603465 to GO:0080139
  * Copied GO:0080139 to GO:0015562 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080139
* Populated new object GO:0080140 (macro)
  * Changed name of GO:0080140 from "<new term>" to "regulation of jasmonic acid metabolic process"
  * Set definition of GO:0080140 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving jasmonic acid."
  * Added definition dbxref GOC:DHL to GO:0080140
  * Copied GO:0080140 to GO:0019217 with type OBO_REL:is_a
  * Copied GO:0080140 to GO:0009694 with type regulates
  * Assigned namespace "biological_process" to GO:0080140
* Populated new object GO:0080141 (macro)
  * Changed name of GO:0080141 from "<new term>" to "regulation of jasmonic acid biosynthetic process"
  * Set definition of GO:0080141 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of jasmonic acid."
  * Added definition dbxref GOC:DHL to GO:0080141
  * Copied GO:0080141 to GO:0009695 with type regulates
  * Copied GO:0080141 to GO:0080140 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0080141
* Populated new object GO:0080142 (macro)
  * Changed name of GO:0080142 from "<new term>" to "regulation of salicylic acid biosynthetic process"
  * Set definition of GO:0080142 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of salicylic acid."
  * Added definition dbxref GOC:DHL to GO:0080142
  * Copied GO:0080142 to GO:0010337 with type OBO_REL:is_a
  * Copied GO:0080142 to GO:0009697 with type regulates
  * Assigned namespace "biological_process" to GO:0080142
* Changed definition of GO:0000418 from "RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The IVa and IVb complexes contain different forms of the largest subunit. The remainder of the complex is composed of smaller subunits." to "RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants. In addition to RNA polymerases I, II, and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, Pol IV and Pol V, that play nonredundant roles in siRNA-directed DNA methylation and gene silencing. Pol IV is required for siRNA production and Pol V is required for generating noncoding transcripts at target loci. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases."
* Added definition dbxref PMID:19110459 to GO:0000418
* Deleted GO:0060497 --OBO_REL:is_a--> GO:0007267
* Copied GO:0060497 to GO:0060638 with type OBO_REL:is_a
* Changed name of GO:0060611 from "mammary gland fat pad development" to "mammary gland fat development"
* Changed definition of GO:0060611 from "The progression of the mammary gland fat pad over time, from its formation to the mature structure. The mammary fat pads are adipose structures in the gland that are invaded by the mammary ducts." to "The progression of the mammary gland fat over time, from its formation to the mature structure. The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts."
* Changed name of GO:0060617 from "mesenchymal-epithelial signaling involved in mammary placode formation" to "positive regulation of mammary placode formation by mesenchymal-epithelial signaling"
* Deleted GO:0060617 --part_of--> GO:0060596
* Deleted GO:0060617 --OBO_REL:is_a--> GO:0007267
* Copied GO:0060617 to GO:0051094 with type OBO_REL:is_a
* Copied GO:0060617 to GO:0060596 with type positively_regulates
* Copied GO:0060617 to GO:0060638 with type OBO_REL:is_a
* Copied GO:0060617 to GO:0051240 with type OBO_REL:is_a