[Go-diff] GO update 07/23/2008

Wed Jul 23 21:30:47 PDT 2008

OBODIFF of gene_ontology_write.obo version 1.139 by 1.140

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034606
* Created object of type obo:TERM with id GO:0034607
* Created object of type obo:TERM with id GO:0034608
* Created object of type obo:TERM with id GO:0034609
* Created object of type obo:TERM with id GO:0034610
* Created object of type obo:TERM with id GO:0034611
* Created object of type obo:TERM with id GO:0034612
* Created object of type obo:TERM with id GO:0034613
* Populated new object GO:0034606 (macro)
  * Changed name of GO:0034606 from "<new term>" to "response to hermaphrodite contact"
  * Set definition of GO:0034606 to "The response by the male to a hermaphrodite after initial contact following mate finding. The male stops forward locomotion, presses the ventral side of his tail against his partner's body, and begins moving backward along the hermaphrodite. Male response behavior is initiated when sensory neurons located in the rays of his tail contact a potential mate."
  * Added definition dbxref PMID:18050467 to GO:0034606
  * Added definition dbxref WB_REF:WBPaper00002109 to GO:0034606
  * Copied GO:0034606 to GO:0060179 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034606
* Populated new object GO:0034607 (macro)
  * Changed name of GO:0034607 from "<new term>" to "turning behavior involved in mating"
  * Set definition of GO:0034607 to "The sharp ventral turn performed by the male as he approaches either the hermaphrodite head or tail, whilst trying to locate his partner's vulva. Turning occurs via a sharp ventral coil of the male's tail."
  * Added definition dbxref PMID:18050467 to GO:0034607
  * Added definition dbxref WB_REF:WBPaper00002109 to GO:0034607
  * Added synonym "turning behavior during mating" to GO:0034607
  * Changed synonym scope of GO:0034607 from "Related" to "Exact"
  * Copied GO:0034607 to GO:0060179 with type OBO_REL:is_a
  * Copied GO:0034607 to GO:0035178 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034607
* Populated new object GO:0034608 (macro)
  * Changed name of GO:0034608 from "<new term>" to "vulval location"
  * Set definition of GO:0034608 to "Location, by the male, of his partner's vulva when backing along the ventral side of the hermaphrodite during mating. The male stops at
the vulva, coordinates his movements to the hermaphrodite's, and
positions his tail precisely over the vulva so that he may insert his spicules and ejaculate."
  * Added definition dbxref PMID:18050467 to GO:0034608
  * Copied GO:0034608 to GO:0060179 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034608
* Populated new object GO:0034609 (macro)
  * Changed name of GO:0034609 from "<new term>" to "spicule insertion"
  * Set definition of GO:0034609 to "Insertion of the male copulatory spicules into the hermaphrodite. Spicule insertion behavior initiates when the male cloaca contacts the vulva. During most mating encounters, the spicule tips will prod the vulva continuously until they partially penetrate, which then causes the protractors to contract completely so that the spicules extend through the vulva."
  * Added definition dbxref PMID:18050467 to GO:0034609
  * Copied GO:0034609 to GO:0060179 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034609
* Populated new object GO:0034610 (macro)
  * Changed name of GO:0034610 from "<new term>" to "oligodeoxyribonucleotidase activity"
  * Set definition of GO:0034610 to "Catalysis of the exonucleolytic cleavage of oligodeoxyribonucleotides to yield deoxyribonucleoside 5'-phosphates."
  * Added definition dbxref GOC:mah to GO:0034610
  * Added synonym "DNA oligonucleotidase activity" to GO:0034610
  * Changed synonym scope of GO:0034610 from "Related" to "Exact"
  * Copied GO:0034610 to GO:0004536 with type OBO_REL:is_a
  * Copied GO:0034610 to GO:0008946 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034610
* Populated new object GO:0034611 (macro)
  * Changed name of GO:0034611 from "<new term>" to "oligoribonucleotidase activity"
  * Set definition of GO:0034611 to "Catalysis of the exonucleolytic cleavage of oligoribonucleotides to yield ribonucleoside 5'-phosphates."
  * Added definition dbxref GOC:mah to GO:0034611
  * Added synonym "RNA oligonucleotidase activity" to GO:0034611
  * Changed synonym scope of GO:0034611 from "Related" to "Exact"
  * Copied GO:0034611 to GO:0008946 with type OBO_REL:is_a
  * Copied GO:0034611 to GO:0004540 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034611
* Populated new object GO:0034612 (macro)
  * Changed name of GO:0034612 from "<new term>" to "response to tumor necrosis factor"
  * Set definition of GO:0034612 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 tumor necrosis factor stimulus."
  * Added definition dbxref GOC:mah to GO:0034612
  * Added synonym "response to TNF" to GO:0034612
  * Changed synonym scope of GO:0034612 from "Related" to "Exact"
  * Copied GO:0034612 to GO:0034097 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034612
* Populated new object GO:0034613 (macro)
  * Changed name of GO:0034613 from "<new term>" to "cellular protein localization"
  * Set definition of GO:0034613 to "Any process by which a protein is transported to, and/or maintained in, a specific location within or at the surface of a cell."
  * Added definition dbxref GOC:mah to GO:0034613
  * Copied GO:0034613 to GO:0008104 with type OBO_REL:is_a
  * Copied GO:0034613 to GO:0051641 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034613
* Changed definition of GO:0000172 from "A ribonucleoprotein complex that performs the first cleavage in rRNA transcript processing and is also involved in mitochondrial RNA processing." to "A ribonucleoprotein complex that cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication."
* Added definition dbxref GOC:sgd_curators to GO:0000172
* Added definition dbxref PMID:14729943 to GO:0000172
* Added definition dbxref PMID:7510714 to GO:0000172
* Deleted GO:0000172 --OBO_REL:is_a--> GO:0030529
* Copied GO:0000172 to GO:0005732 with type OBO_REL:is_a
* Changed definition of GO:0000957 from "The chemical reactions and pathways resulting in the breakdown of RNA within the mitochondrion." to "The chemical reactions and pathways resulting in the breakdown of RNA transcribed from the mitochondrial genome and occurring in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000957
* Changed definition of GO:0000958 from "The chemical reactions and pathways resulting in the breakdown of mRNA within the mitochondrion." to "The chemical reactions and pathways resulting in the breakdown of mRNA transcribed from the mitochondrial genome and occurring in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000958
* Changed definition of GO:0000959 from "The chemical reactions and pathways involving RNA in the mitochondrion." to "The chemical reactions and pathways involving RNA transcribed from the mitochondrial genome and occurring in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000959
* Changed definition of GO:0000960 from "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catabolism of RNA within the mitochondrion." to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome."
* Added definition dbxref GOC:mah to GO:0000960
* Changed definition of GO:0000961 from "Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways involving catabolism of RNA within the mitochondrion." to "Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome."
* Added definition dbxref GOC:mah to GO:0000961
* Changed definition of GO:0000962 from "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism of RNA within the mitochondrion." to "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome."
* Added definition dbxref GOC:mah to GO:0000962
* Changed definition of GO:0000963 from "The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules." to "The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules; occurs in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000963
* Changed definition of GO:0000964 from "Any process involved in forming the mature 5' end of an RNA molecule transcribed from a mitochondrial genome." to "Any process involved in forming the mature 5' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000964
* Changed definition of GO:0000965 from "Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome." to "Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000965
* Added comment "Note that enzymes with this activity also act on D-glucitol (giving D-fructose) and other closely related sugar alcohols."
* Added synonym " L-iditol:NAD+ 5-oxidoreductase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym  L-iditol:NAD+ 5-oxidoreductase activity of GO:0003939
* Changed synonym scope of GO:0003939 from "Related" to "Exact"
* Added synonym "L-iditol (sorbitol) dehydrogenase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym L-iditol (sorbitol) dehydrogenase activity of GO:0003939
* Added synonym "L-iditol:NAD oxidoreductase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym L-iditol:NAD oxidoreductase activity of GO:0003939
* Changed synonym scope of GO:0003939 from "Related" to "Exact"
* Added synonym "NAD+-dependent sorbitol dehydrogenase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym NAD+-dependent sorbitol dehydrogenase activity of GO:0003939
* Added synonym "NAD-dependent sorbitol dehydrogenase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym NAD-dependent sorbitol dehydrogenase activity of GO:0003939
* Added synonym "NAD-sorbitol dehydrogenase" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym NAD-sorbitol dehydrogenase of GO:0003939
* Deleted GO:0005732 --OBO_REL:is_a--> GO:0044452
* Copied GO:0005732 to GO:0044424 with type OBO_REL:is_a
* Deleted GO:0007035 --part_of--> GO:0007033
* Copied GO:0007569 to GO:0009987 with type OBO_REL:is_a
* Added comment "Note that enzymes with this activity usually also hydrolyze NAD+ to NMN and AMP."
* Changed definition of GO:0008946 from "Catalysis of the exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates; also hydrolyzes NAD+ to NMN and AMP." to "Catalysis of the exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates."
* Deleted synonym "oligoribonuclease activity" from GO:0008946
* Deleted GO:0008946 --OBO_REL:is_a--> GO:0016895
* Deleted GO:0008946 --OBO_REL:is_a--> GO:0004540
* Copied GO:0008946 to GO:0004518 with type OBO_REL:is_a
* Deleted GO:0010621 --OBO_REL:is_a--> GO:0008104
* Copied GO:0010621 to GO:0034613 with type OBO_REL:is_a
* Copied GO:0016192 to GO:0009987 with type OBO_REL:is_a
* Changed definition of GO:0030686 from "A preribosomal complex consisting of the 35S pre-rRNA, the 5S rRNA, early-associating ribosomal proteins, and associated proteins." to "A large ribonucleoprotein complex considered to be the earliest preribosomal complex. In S. cerevisiae, it has a size of 90S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins."
* Deleted definition dbxref PMID:10567516 from GO:0030686
* Added definition dbxref PMID:12150911 to GO:0030686
* Added definition dbxref PMID:12957375 to GO:0030686
* Added definition dbxref PMID:15120992 to GO:0030686
* Copied GO:0031428 to GO:0044452 with type OBO_REL:is_a
* Copied GO:0031429 to GO:0044452 with type OBO_REL:is_a
* Changed definition of GO:0032040 from "A large ribonuclear protein complex containing the U3 snoRNA and associated proteins (28 in S. cerevisiae) that is involved in processing of the pre-18S rRNA to form the small ribosomal subunit." to "A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins."
* Added definition dbxref PMID:12957375 to GO:0032040
* Added definition dbxref PMID:15120992 to GO:0032040
* Added definition dbxref PMID:15590835 to GO:0032040
* Deleted GO:0033365 --OBO_REL:is_a--> GO:0008104
* Copied GO:0033365 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0034394 --OBO_REL:is_a--> GO:0008104
* Copied GO:0034394 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0034497 --OBO_REL:is_a--> GO:0008104
* Copied GO:0034497 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0034501 --OBO_REL:is_a--> GO:0008104
* Copied GO:0034501 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0034502 --OBO_REL:is_a--> GO:0008104
* Copied GO:0034502 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0051205 --OBO_REL:is_a--> GO:0008104
* Copied GO:0051205 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0051641 --OBO_REL:is_a--> GO:0016043
* Copied GO:0051641 to GO:0009987 with type OBO_REL:is_a
* Copied GO:0055085 to GO:0009987 with type OBO_REL:is_a