[Go-diff] GO update 03/30/2009

[Remote CVS for Gene Ontology]

OBODIFF of gene_ontology_write.obo version 1.499 by 1.503

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0060462
* Created object of type obo:TERM with id GO:0060463
* Created object of type obo:TERM with id GO:0060464
* Created object of type obo:TERM with id GO:0070530
* Created object of type obo:TERM with id GO:0070531
* Created object of type obo:TERM with id GO:0070532
* Created object of type obo:TERM with id GO:0070533
* Created object of type obo:TERM with id GO:0070534
* Created object of type obo:TERM with id GO:0070535
* Created object of type obo:TERM with id GO:0070536
* Created object of type obo:TERM with id GO:0070537
* Populated new object GO:0060462 (macro)
  * Changed name of GO:0060462 from "<new term>" to "lung lobe development"
  * Set definition of GO:0060462 to "The process whose specific outcome is the progression of a lung lode over time, from its formation to the mature structure. A lung lobe is a projection that extends from the lung."
  * Added definition dbxref GOC:dph to GO:0060462
  * Copied GO:0060462 to GO:0048856 with type OBO_REL:is_a
  * Copied GO:0060462 to GO:0030324 with type part_of
  * Assigned namespace "biological_process" to GO:0060462
* Populated new object GO:0060463 (macro)
  * Changed name of GO:0060463 from "<new term>" to "lung lobe morphogenesis"
  * Set definition of GO:0060463 to "The process by which the anatomical structures of a lung lobe are generated and organized. Morphogenesis pertains to the creation of form. A lung lobe is a projection that extends from the lung."
  * Added definition dbxref GOC:dph to GO:0060463
  * Copied GO:0060463 to GO:0060425 with type part_of
  * Copied GO:0060463 to GO:0060462 with type part_of
  * Copied GO:0060463 to GO:0009653 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060463
* Populated new object GO:0060464 (macro)
  * Changed name of GO:0060464 from "<new term>" to "lung lobe formation"
  * Set definition of GO:0060464 to "The developmental process pertaining to the initial formation of a lung lobe from unspecified parts. This process begins with the specific processes that contribute to the appearance of the lobe and ends when the structural rudiment is recognizable. A lung lobe is a projection that extends from the lung."
  * Added definition dbxref GOC:dph to GO:0060464
  * Copied GO:0060464 to GO:0048646 with type OBO_REL:is_a
  * Copied GO:0060464 to GO:0060463 with type part_of
  * Assigned namespace "biological_process" to GO:0060464
* Populated new object GO:0070530 (macro)
  * Changed name of GO:0070530 from "<new term>" to "K63-linked polyubiquitin binding"
  * Set definition of GO:0070530 to "Interacting selectively and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers."
  * Added definition dbxref GOC:mah to GO:0070530
  * Added definition dbxref PMID:15556404 to GO:0070530
  * Added definition dbxref PMID:17525341 to GO:0070530
  * Copied GO:0070530 to GO:0031593 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070530
* Populated new object GO:0070531 (macro)
  * Changed name of GO:0070531 from "<new term>" to "BRCA1-A complex"
  * Set definition of GO:0070531 to "A protein complex that contains the BRCA1-BARD1 heterodimer, RAP80/UIMC1, BRCC3/BRCC36, BRE/BRCC45, FAM175A/CCDC98/Abraxas and MERIT40/NBA1, and specifically recognizes and binds K63-linked polyubiquitin chains present on histone H2A and H2AX at DNA damage sites."
  * Added definition dbxref GOC:mah to GO:0070531
  * Added definition dbxref PMID:19261749 to GO:0070531
  * Copied GO:0070531 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0070531 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070531
* Populated new object GO:0070532 (macro)
  * Changed name of GO:0070532 from "<new term>" to "BRCA1-B complex"
  * Set definition of GO:0070532 to "A protein complex that contains the BRCA1-BARD1 heterodimer, BACH1 and TopBP1, and binds to DNA during S phase at DNA damage sites."
  * Added definition dbxref GOC:mah to GO:0070532
  * Added definition dbxref PMID:16391231 to GO:0070532
  * Copied GO:0070532 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0070532 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070532
* Populated new object GO:0070533 (macro)
  * Changed name of GO:0070533 from "<new term>" to "BRCA1-C complex"
  * Set definition of GO:0070533 to "A protein complex that contains the BRCA1-BARD1 heterodimer, CtIP and Mre11/Rad50/NBS1 (M/R/N) complex, and binds to DNA at DNA damage sites. BRCA1-C binding ta damaged DNA is required for DNA damage-induced Chk1 phosphorylation and the G2/M transition checkpoint."
  * Added definition dbxref GOC:mah to GO:0070533
  * Added definition dbxref PMID:15485915 to GO:0070533
  * Added definition dbxref PMID:16391231 to GO:0070533
  * Copied GO:0070533 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0070533 to GO:0044428 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070533
* Populated new object GO:0070534 (macro)
  * Changed name of GO:0070534 from "<new term>" to "protein K63-linked ubiquitination"
  * Set definition of GO:0070534 to "A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair."
  * Added definition dbxref GOC:mah to GO:0070534
  * Added definition dbxref PMID:15556404 to GO:0070534
  * Copied GO:0070534 to GO:0016567 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070534
* Populated new object GO:0070535 (macro)
  * Changed name of GO:0070535 from "<new term>" to "histone H2A K63-linked ubiquitination"
  * Set definition of GO:0070535 to "A histone ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a lysine residue in histone H2A or the variant H2AX."
  * Added definition dbxref GOC:mah to GO:0070535
  * Added definition dbxref PMID:18430235 to GO:0070535
  * Copied GO:0070535 to GO:0033522 with type OBO_REL:is_a
  * Copied GO:0070535 to GO:0070534 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070535
* Populated new object GO:0070536 (macro)
  * Changed name of GO:0070536 from "<new term>" to "protein K63-linked deubiquitination"
  * Set definition of GO:0070536 to "A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a protein."
  * Added definition dbxref GOC:mah to GO:0070536
  * Added definition dbxref PMID:19202061 to GO:0070536
  * Added definition dbxref PMID:19214193 to GO:0070536
  * Copied GO:0070536 to GO:0016579 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070536
* Populated new object GO:0070537 (macro)
  * Changed name of GO:0070537 from "<new term>" to "histone H2A K63-linked deubiquitination"
  * Set definition of GO:0070537 to "A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a lysine residue in histone H2A or the variant H2AX."
  * Added definition dbxref GOC:mah to GO:0070537
  * Added definition dbxref PMID:19202061 to GO:0070537
  * Added definition dbxref PMID:19214193 to GO:0070537
  * Copied GO:0070537 to GO:0016578 with type OBO_REL:is_a
  * Copied GO:0070537 to GO:0070536 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070537
* Copied GO:0002052 to GO:0050769 with type OBO_REL:is_a
* Deleted GO:0006413 --OBO_REL:is_a--> GO:0022618
* Copied GO:0006413 to GO:0009987 with type OBO_REL:is_a
* Deleted GO:0006446 --OBO_REL:is_a--> GO:0051128
* Copied GO:0006446 to GO:0050794 with type OBO_REL:is_a
* Copied GO:0007317 to GO:0044087 with type OBO_REL:is_a
* Copied GO:0010104 to GO:0070297 with type OBO_REL:is_a
* Copied GO:0010105 to GO:0070298 with type OBO_REL:is_a
* Copied GO:0010522 to GO:0032844 with type OBO_REL:is_a
* Copied GO:0010522 to GO:0050794 with type OBO_REL:is_a
* Copied GO:0010523 to GO:0048523 with type OBO_REL:is_a
* Copied GO:0010523 to GO:0032845 with type OBO_REL:is_a
* Copied GO:0010524 to GO:0048522 with type OBO_REL:is_a
* Copied GO:0010524 to GO:0032846 with type OBO_REL:is_a
* Copied GO:0010695 to GO:0070507 with type OBO_REL:is_a
* Copied GO:0010847 to GO:0044087 with type OBO_REL:is_a
* Added general dbxref GOC:mah to synonym spinal cord dorsal-ventral patterning of GO:0021513
* Added general dbxref GOC:mah to synonym forebrain dorsal-ventral pattern formation of GO:0021798
* Deleted GO:0031498 --OBO_REL:is_a--> GO:0043624
* Copied GO:0031498 to GO:0022411 with type OBO_REL:is_a
* Changed definition of GO:0033522 from "The modification of histone H2A by addition of ubiquitin groups. Modification occurs at lysine 119 (H2A-K119) of metazoans or the equivalent residue." to "The modification of histone H2A by addition of ubiquitin groups. Steady-state modification occurs at lysine 119 (H2A-K119) of metazoans or the equivalent residue; during double-strand break repair, modification may also occur at additional H2A lysine residues."
* Added definition dbxref PMID:18430235 to GO:0033522
* Copied GO:0045855 to GO:0044087 with type OBO_REL:is_a
* Copied GO:0045856 to GO:0044089 with type OBO_REL:is_a
* Deleted GO:0045947 --OBO_REL:is_a--> GO:0051129
* Copied GO:0045947 to GO:0048523 with type OBO_REL:is_a
* Deleted GO:0045948 --OBO_REL:is_a--> GO:0051130
* Copied GO:0045948 to GO:0048522 with type OBO_REL:is_a
* Removed comment