[Go-diff] GO update 06/11/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Wed Jun 11 21:30:52 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.104 by 1.105

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034505
* Created object of type obo:TERM with id GO:0034506
* Created object of type obo:TERM with id GO:0034507
* Created object of type obo:TERM with id GO:0034508
* Created object of type obo:TERM with id GO:0034509
* Populated new object GO:0034505 (macro)
  * Changed name of GO:0034505 from "<new term>" to "tooth mineralization"
  * Set definition of GO:0034505 to "The process by which calcium salts are deposited into calcareous tooth structure such as dental enamel, dentin and cementum."
  * Added definition dbxref GOC:mah to GO:0034505
  * Added definition dbxref MESH:tooth+calcification to GO:0034505
  * Added definition dbxref MP:0002817 to GO:0034505
  * Added synonym "tooth calcification" to GO:0034505
  * Changed synonym scope of GO:0034505 from "Related" to "Exact"
  * Copied GO:0034505 to GO:0042476 with type part_of
  * Copied GO:0034505 to GO:0031214 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034505
* Populated new object GO:0034506 (macro)
  * Changed name of GO:0034506 from "<new term>" to "chromosome, centromeric core region"
  * Set definition of GO:0034506 to "The innermost portion of the centromeric region of a chromosome, encompassing the core region of a chromosome centromere and the proteins that bind to it."
  * Added definition dbxref GOC:mah to GO:0034506
  * Added definition dbxref GOC:val to GO:0034506
  * Added synonym "chromosome, centric core region" to GO:0034506
  * Copied GO:0034506 to GO:0000775 with type part_of
  * Copied GO:0034506 to GO:0044427 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034506
* Populated new object GO:0034507 (macro)
  * Changed name of GO:0034507 from "<new term>" to "chromosome, centromeric outer repeat region"
  * Set definition of GO:0034507 to "The portion of the centromeric region of a chromosome that flanks the core region, encompassing repeated regions of a chromosome centromere and the proteins that bind to it."
  * Added definition dbxref GOC:mah to GO:0034507
  * Added definition dbxref GOC:val to GO:0034507
  * Added synonym "chromosome, centric outer repeat region" to GO:0034507
  * Copied GO:0034507 to GO:0000775 with type part_of
  * Copied GO:0034507 to GO:0044427 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034507
* Populated new object GO:0034508 (macro)
  * Changed name of GO:0034508 from "<new term>" to "centromere complex assembly"
  * Set definition of GO:0034508 to "The aggregation, arrangement and bonding together of proteins and centromeric DNA molecules to form a centromeric protein-DNA complex. Includes the formation of the chromatin structures which form a platform for the kinetochore, and assembly of the kinetochore onto this specialzed chromatin. In fission yeast and higher eukaryotes this process also includes the formation of heterochromatin at the outer repeat (pericentric) regions of the centromere."
  * Added definition dbxref GOC:mah to GO:0034508
  * Added definition dbxref GOC:vw to GO:0034508
  * Copied GO:0034508 to GO:0051276 with type OBO_REL:is_a
  * Copied GO:0034508 to GO:0065004 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034508
* Populated new object GO:0034509 (macro)
  * Changed name of GO:0034509 from "<new term>" to "centromeric core chromatin formation"
  * Set definition of GO:0034509 to "The assembly of chromatin into the specialized structure characteristic of the centromeric core region, defined by the presence of the variant histone CENP-A."
  * Added definition dbxref GOC:mah to GO:0034509
  * Added definition dbxref GOC:vw to GO:0034509
  * Added synonym "centric core chromatin formation" to GO:0034509
  * Changed synonym scope of GO:0034509 from "Related" to "Exact"
  * Added synonym "centromeric core chromatin assembly" to GO:0034509
  * Changed synonym scope of GO:0034509 from "Related" to "Exact"
  * Copied GO:0034509 to GO:0031497 with type OBO_REL:is_a
  * Copied GO:0034509 to GO:0034508 with type part_of
  * Assigned namespace "biological_process" to GO:0034509
* Changed synonym scope of GO:0000500 from "Broad" to "Exact"
* Changed name of GO:0000775 from "chromosome, pericentric region" to "chromosome, centromeric region"
* Changed definition of GO:0000775 from "The central region of a chromosome that includes the centromere and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." to "The region of a chromosome that includes the centromere and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome."
* Added synonym "chromosome, centric region" to GO:0000775
* Changed synonym scope of GO:0000775 from "Related" to "Exact"
* Added synonym "chromosome, pericentric region" to GO:0000775
* Changed definition of GO:0000776 from "A multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules." to "A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules."
* Changed definition of GO:0000777 from "A multisubunit complex that is located at the pericentric region of a condensed chromosome and provides an attachment point for the spindle microtubules." to "A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules."
* Changed definition of GO:0000778 from "A multisubunit complex that is located at the pericentric region of a condensed chromosome in the nucleus and provides an attachment point for the spindle microtubules." to "A multisubunit complex that is located at the centromeric region of a condensed chromosome in the nucleus and provides an attachment point for the spindle microtubules."
* Changed name of GO:0000779 from "condensed chromosome, pericentric region" to "condensed chromosome, centromeric region"
* Changed definition of GO:0000779 from "The central region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." to "The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome."
* Added synonym "condensed chromosome, centric region" to GO:0000779
* Changed synonym scope of GO:0000779 from "Related" to "Exact"
* Added synonym "condensed chromosome, pericentric region" to GO:0000779
* Changed name of GO:0000780 from "condensed nuclear chromosome, pericentric region" to "condensed nuclear chromosome, centromeric region"
* Changed definition of GO:0000780 from "The central region of a condensed chromosome in the nucleus that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." to "The region of a condensed chromosome in the nucleus that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome."
* Added synonym "condensed nuclear chromosome, centric region" to GO:0000780
* Changed synonym scope of GO:0000780 from "Related" to "Exact"
* Added synonym "condensed nuclear chromosome, pericentric region" to GO:0000780
* Added synonym "CTP:diacylglycerol kinase activity" to GO:0004143
* Changed synonym scope of GO:0004143 from "Related" to "Narrow"
* Changed name of GO:0005721 from "centric heterochromatin" to "centromeric heterochromatin"
* Deleted synonym "centromeric heterochromatin" from GO:0005721
* Added synonym "centric heterochromatin" to GO:0005721
* Changed synonym scope of GO:0005721 from "Related" to "Exact"
* Copied GO:0006260 to GO:0043284 with type OBO_REL:is_a
* Added synonym "RNA-protein complex biogenesis and assembly" to GO:0022613
* Changed synonym scope of GO:0022613 from "Related" to "Exact"
* Added synonym "biomineralization" to GO:0031214
* Changed synonym scope of GO:0031214 from "Related" to "Exact"
* Changed name of GO:0031508 from "centric heterochromatin formation" to "centromeric heterochromatin formation"
* Deleted synonym "centric heterochromatin assembly" from GO:0031508
* Deleted synonym "centromeric heterochromatin formation" from GO:0031508
* Added synonym "centric heterochromatin formation" to GO:0031508
* Changed synonym scope of GO:0031508 from "Related" to "Exact"
* Added synonym "centromeric heterochromatin assembly" to GO:0031508
* Changed synonym scope of GO:0031508 from "Related" to "Exact"
* Copied GO:0031508 to GO:0034508 with type part_of
* Changed name of GO:0031618 from "nuclear centric heterochromatin" to "nuclear centromeric heterochromatin"
* Added synonym "nuclear centric heterochromatin" to GO:0031618
* Changed synonym scope of GO:0031618 from "Related" to "Exact"
* Deleted GO:0032040 --OBO_REL:is_a--> GO:0030529
* Deleted GO:0032040 --OBO_REL:is_a--> GO:0044452
* Copied GO:0032040 to GO:0030685 with type OBO_REL:is_a
* Changed name of GO:0042475 from "odontogenesis of dentine-containing teeth" to "odontogenesis of dentine-containing tooth"
* Changed definition of GO:0042475 from "The process whose specific outcome is the progression of a tooth over time, from its formation to the mature structure. Teeth are the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates, and which usually aid in the prehension and mastication of food." to "The process whose specific outcome is the progression of a dentine-containing tooth over time, from its formation to the mature structure. A dentine-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and are composed mainly of dentine, a dense calcified substance, covered by a layer of enamel."
* Deleted definition dbxref GOC:jl from GO:0042475
* Deleted definition dbxref MetaCyc:THRESYN-PWY from GO:0042475
* Added definition dbxref GOC:mah to GO:0042475
* Added definition dbxref PMID:10333884 to GO:0042475
* Added synonym "odontogenesis of dentine-containing teeth" to GO:0042475
* Changed synonym scope of GO:0042475 from "Related" to "Exact"
* added secondary id GO:0042477 to GO:0042476
* Changed definition of GO:0042476 from "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s)." to "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food."
* Added definition dbxref GOC:mah to GO:0042476
* Added synonym "odontogenesis (sensu Protostomia)" to GO:0042476
* Changed synonym scope of GO:0042476 from "Related" to "Narrow"
* Added synonym "odontogenesis of calcareous or chitinous tooth" to GO:0042476
* Changed synonym scope of GO:0042476 from "Related" to "Narrow"
* Added synonym "tooth development (sensu Invertebrata)" to GO:0042476
* Changed synonym scope of GO:0042476 from "Related" to "Narrow"
* Deleted GO:0042477 --OBO_REL:is_a--> GO:0042476
* Deleted GO:0042484 --regulates--> GO:0042477
* Deleted GO:0042485 --positively_regulates--> GO:0042477
* Deleted GO:0042486 --negatively_regulates--> GO:0042477
* Destroyed object GO:0042477
* added secondary id GO:0042484 to GO:0042481
* Added synonym "regulation of odontogenesis (sensu Protostomia)" to GO:0042481
* Changed synonym scope of GO:0042481 from "Related" to "Narrow"
* Added synonym "regulation of odontogenesis of calcareous or chitinous tooth" to GO:0042481
* Changed synonym scope of GO:0042481 from "Related" to "Narrow"
* Added synonym "regulation of tooth development" to GO:0042481
* Changed synonym scope of GO:0042481 from "Related" to "Exact"
* added secondary id GO:0042485 to GO:0042482
* Added synonym "activation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "positive regulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Exact"
* Added synonym "positive regulation of odontogenesis of calcareous or chitinous tooth" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "positive regulation of tooth development" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Exact"
* Added synonym "stimulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "up regulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "up-regulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* Added synonym "upregulation of odontogenesis (sensu Protostomia)" to GO:0042482
* Changed synonym scope of GO:0042482 from "Related" to "Narrow"
* added secondary id GO:0042486 to GO:0042483
* Added synonym "down regulation of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "down-regulation of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "downregulation of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "inhibition of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "negative regulation of odontogenesis (sensu Protostomia)" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "negative regulation of odontogenesis of calcareous or chitinous tooth" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Narrow"
* Added synonym "negative regulation of tooth development" to GO:0042483
* Changed synonym scope of GO:0042483 from "Related" to "Exact"
* Deleted GO:0042484 --regulates--> GO:0042477
* Deleted GO:0042484 --OBO_REL:is_a--> GO:0042481
* Deleted GO:0042486 --OBO_REL:is_a--> GO:0042484
* Deleted GO:0042485 --OBO_REL:is_a--> GO:0042484
* Destroyed object GO:0042484
* Deleted GO:0042485 --OBO_REL:is_a--> GO:0042482
* Deleted GO:0042485 --positively_regulates--> GO:0042477
* Deleted GO:0042485 --OBO_REL:is_a--> GO:0042484
* Destroyed object GO:0042485
* Deleted GO:0042486 --OBO_REL:is_a--> GO:0042484
* Deleted GO:0042486 --OBO_REL:is_a--> GO:0042483
* Deleted GO:0042486 --negatively_regulates--> GO:0042477
* Destroyed object GO:0042486
* Changed name of GO:0042487 from "regulation of odontogenesis of dentine-containing teeth" to "regulation of odontogenesis of dentine-containing tooth"
* Added synonym "regulation of odontogenesis of dentine-containing teeth" to GO:0042487
* Changed synonym scope of GO:0042487 from "Related" to "Exact"
* Changed name of GO:0042488 from "positive regulation of odontogenesis of dentine-containing teeth" to "positive regulation of odontogenesis of dentine-containing tooth"
* Added synonym "positive regulation of odontogenesis of dentine-containing teeth" to GO:0042488
* Changed synonym scope of GO:0042488 from "Related" to "Exact"
* Changed name of GO:0042489 from "negative regulation of odontogenesis of dentine-containing teeth" to "negative regulation of odontogenesis of dentine-containing tooth"
* Added synonym "negative regulation of odontogenesis of dentine-containing teeth" to GO:0042489
* Changed synonym scope of GO:0042489 from "Related" to "Exact"
* Changed definition of GO:0051382 from "The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules." to "The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules."
* Copied GO:0051382 to GO:0034508 with type part_of
* Changed definition of GO:0051383 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the kinetochore, a multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules."

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