[Go-diff] GO update 06/24/2009

[Remote CVS for Gene Ontology]

OBODIFF of gene_ontology_write.obo version 1.678 by 1.680

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0011000
* Created object of type obo:TERM with id GO:0090001
* Populated new object GO:0011000 (macro)
  * Changed name of GO:0011000 from "<new term>" to "replication fork arrest at mating type locus"
  * Set definition of GO:0011000 to "A process that impedes the progress of the DNA replication fork at natural replication fork pausing sites within the mating type locus."
  * Added definition dbxref GOC:dph to GO:0011000
  * Added definition dbxref GOC:tb to GO:0011000
  * Copied GO:0011000 to GO:0043111 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0011000
* Populated new object GO:0090001 (macro)
  * Changed name of GO:0090001 from "<new term>" to "replication fork arrest at tRNA locus"
  * Set definition of GO:0090001 to "A process that impedes the progress of the DNA replication fork at natural replication fork pausing sites within the eukaryotic tRNA transcription unit."
  * Added definition dbxref GOC:dph to GO:0090001
  * Added definition dbxref GOC:tb to GO:0090001
  * Copied GO:0090001 to GO:0043111 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0090001
* Added general dbxref G2-specific transcription in mitotic cell cycle (Reactome:69957) to GO:0000116
* Added comment "Consider also annotating to the molecular function term 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906'."
* Changed definition of GO:0000703 from "Catalysis of the formation of a covalent enzyme-pyrimidine base intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apyrimidinic (AP) site. Enzymes with this activity recognize and remove oxidized pyrimidine bases by cleaving the N-C1' glycosidic bond between the oxidized pyrimidine and the deoxyribose sugar." to "Catalysis of the removal oxidized pyrimidine bases by cleaving the N-C1' glycosidic bond between the oxidized pyrimidine and the deoxyribose sugar. The reaction involves formation of a covalent enzyme-pyrimidine base intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apyrimidinic (AP) site."
* Deleted GO:0000703 --OBO_REL:is_a--> GO:0004520
* Deleted GO:0002110 --OBO_REL:is_a--> GO:0016552
* Added comment "Consider also annotating to the molecular function term 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906'."
* Changed definition of GO:0008534 from "Catalysis of the removal of oxidized purine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar. The reaction involves the formation of a covalent enzyme substrate intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apurinic (AP) site." to "Catalysis of the removal of oxidized purine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar. The reaction involves the formation of a covalent enzyme-substrate intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apurinic (AP) site."
* Deleted GO:0008534 --OBO_REL:is_a--> GO:0004520
* Added comment "This term was made obsolete because it represents two separate processes (insertion and deletion)."
* Changed definition of GO:0016550 from "The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place during or after transcription." to "OBSOLETE. The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place during or after transcription."
* Removed GO:0016550 from category gosubset_prok
* Deleted GO:0016550 --OBO_REL:is_a--> GO:0009451
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at fb5548
* Added comment "This term was made obsolete because it represents two separate processes (insertion and deletion)."
* Changed definition of GO:0016551 from "The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place after transcription." to "OBSOLETE. The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place after transcription."
* Removed GO:0016551 from category gosubset_prok
* Deleted GO:0016551 --OBO_REL:is_a--> GO:0016550
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 9bfefd
* Added comment "This term was made obsolete because it represents two separate processes (insertion and deletion)."
* Changed definition of GO:0016552 from "The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place during transcription." to "OBSOLETE. The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place during transcription."
* Removed GO:0016552 from category gosubset_prok
* Deleted GO:0016552 --OBO_REL:is_a--> GO:0016550
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 1819a82
* Copied GO:0030431 to GO:0007610 with type OBO_REL:is_a
* Added synonym "negative regulation of DNA replication at replication fork barrier" to GO:0043111
* Added general dbxref GOC:tb to synonym negative regulation of DNA replication at replication fork barrier of GO:0043111
* Added general dbxref GOC:dph to synonym negative regulation of DNA replication at replication fork barrier of GO:0043111
* Changed synonym scope of GO:0043111 from "Related" to "Exact"
* Changed definition of GO:0043392 from "Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." to "Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process by which a gene product interacts selectively with DNA (deoxyribonucleic acid)."
* Copied GO:0048757 to GO:0043482 with type OBO_REL:is_a
* Deleted GO:0050931 --OBO_REL:is_a--> GO:0048066
* Copied GO:0050931 to GO:0048066 with type part_of
* Deleted synonym "lung duct secondary branching" from GO:0060599
* Added synonym "mammary gland duct secondary branching" to GO:0060599
* Added general dbxref GOC:dph to synonym mammary gland duct secondary branching of GO:0060599
* Changed synonym scope of GO:0060599 from "Related" to "Exact"