[Go-diff] GO update 04/03/2008

[Remote CVS for Gene Ontology]

OBODIFF of gene_ontology_edit.obo version 5.749 by 5.750

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034357
* Created object of type obo:TERM with id GO:0055114
* Populated new object GO:0034357 (macro)
  * Changed name of GO:0034357 from "<new term>" to "photosynthetic membrane"
  * Set definition of GO:0034357 to "A membrane enriched in complexes formed of reaction centers, accessory pigments and
electron carriers, in which photosynthetic reactions take place."
  * Added definition dbxref GOC:ds to GO:0034357
  * Added definition dbxref GOC:mah to GO:0034357
  * Copied GO:0034357 to GO:0016020 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034357
* Populated new object GO:0055114 (macro)
  * Changed name of GO:0055114 from "<new term>" to "oxidation reduction"
  * Set definition of GO:0055114 to "The process of removal or addition of one or more electrons with or without the concomitant removal or addition of a proton or protons."
  * Added definition dbxref GOC:dl to GO:0055114
  * Added definition dbxref GOC:ed to GO:0055114
  * Added definition dbxref GOC:jid to GO:0055114
  * Added definition dbxref GOC:jm to GO:0055114
  * Added definition dbxref GOC:mlg to GO:0055114
  * Added definition dbxref GOC:rh to GO:0055114
  * Added synonym "electron transport process" to GO:0055114
  * org.geneontology.oboedit.datamodel.history.ChangeSynCategoryHistoryItem at f81c84
  * Changed synonym scope of GO:0055114 from "Related" to "Exact"
  * Added synonym "oxidoreductase process" to GO:0055114
  * org.geneontology.oboedit.datamodel.history.ChangeSynCategoryHistoryItem at 1185f3b
  * Changed synonym scope of GO:0055114 from "Related" to "Exact"
  * Copied GO:0055114 to GO:0008152 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0055114
* Changed name of GO:0001410 from "chlamydospore development" to "chlamydospore formation"
* Changed definition of GO:0001410 from "The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. Chlamydospores are thick-walled, spore-like cells borne on the ends of elongated cells attached to hyphae or pseudohyphae, seen in the species Candida albicans and Candida dubliniensis. Note that although these structures resemble the chlamydospores of other fungi, it is not known whether they are true spores, so this process is not currently considered a type of spore formation." to "The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. A chlamydospores is a mitotic (asexual) one-celled spore, produced primarily for survival, not dispersal, originating endogenously and singly within part of a pre-existing cell and possessing an inner secondary and often thickened cell wall."
* Added definition dbxref ISBN:085199377X to GO:0001410
* Changed synonym scope of GO:0001410 from "Related" to "Narrow"
* Deleted synonym "chlamydospore formation" from GO:0001410
* Added synonym "chlamydospore development" to GO:0001410
* Changed synonym scope of GO:0001410 from "Related" to "Exact"
* Copied GO:0001410 to GO:0030436 with type OBO_REL:is_a
* added secondary id GO:0030090 to GO:0009521
* Changed definition of GO:0009521 from "One of the photochemical systems containing photosynthetic and accessory pigments and electron carriers that operate in sequence to perform the two light reactions of photosynthesis." to "A complex located in a photosynthetic membrane that consists of a photoreaction center associated with accessory pigments and electron carriers."
* Added definition dbxref GOC:ds to GO:0009521
* Added definition dbxref GOC:mah to GO:0009521
* Added definition dbxref PMID:9821949 to GO:0009521
* Added synonym "reaction center (sensu Gram-negative Bacteria)" to GO:0009521
* Changed synonym scope of GO:0009521 from "Related" to "Narrow"
* Added synonym "reaction center (sensu Proteobacteria)" to GO:0009521
* Changed synonym scope of GO:0009521 from "Related" to "Narrow"
* Added synonym "reaction centre (sensu Gram-negative Bacteria)" to GO:0009521
* Changed synonym scope of GO:0009521 from "Related" to "Narrow"
* Added synonym "reaction centre (sensu Proteobacteria)" to GO:0009521
* Changed synonym scope of GO:0009521 from "Related" to "Narrow"
* Deleted GO:0009521 --OBO_REL:is_a--> GO:0044436
* Copied GO:0009521 to GO:0034357 with type part_of
* Changed definition of GO:0009522 from "Photosystem that functions as a light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin to ferredoxin." to "A photosystem that contains an iron-sulfur reaction center associated with accessory pigments and electron carriers. In cyanobacteria and chloroplasts, photosystem I functions as a light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin to ferredoxin; in photosynthetic bacteria that have only a single type I photosystem, such as the green sulfur bacteria, electrons can go either to ferredoxin (Fd) -> NAD+ or to menaquinone (MK) -> Cytb/FeS -> Cytc555 -> photosystem I (cyclic photophosphorylation)."
* Deleted definition dbxref ISBN:0943088399 from GO:0009522
* Added definition dbxref GOC:ds to GO:0009522
* Added definition dbxref GOC:mah to GO:0009522
* Added definition dbxref ISBN:0140514031 to GO:0009522
* Added definition dbxref PMID:9821949 to GO:0009522
* Changed definition of GO:0009523 from "An integral membrane complex containing the P680 reaction center. In the light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone." to "A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers. In cyanobacteria and chloroplasts, in the presence of light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone, whereas other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center."
* Added definition dbxref GOC:ds to GO:0009523
* Added definition dbxref GOC:mah to GO:0009523
* Added definition dbxref PMID:9821949 to GO:0009523
* Deleted GO:0009538 --OBO_REL:is_a--> GO:0044436
* Deleted GO:0009539 --OBO_REL:is_a--> GO:0044436
* Changed definition of GO:0009579 from "A membraneous cellular structure that bears the photosynthetic pigments in photosynthetic organisms. In prokaryotes the thylakoids are of various shapes and are attached to the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." to "A membraneous cellular structure that bears the photosynthetic pigments in photosynthetic organisms. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation."
* Added definition dbxref GOC:ds to GO:0009579
* Deleted GO:0009579 --OBO_REL:is_a--> GO:0043231
* Copied GO:0009579 to GO:0034357 with type OBO_REL:is_a
* Deleted GO:0009782 --OBO_REL:is_a--> GO:0044436
* Deleted GO:0009783 --OBO_REL:is_a--> GO:0044436
* Deleted GO:0009941 --OBO_REL:is_a--> GO:0016020
* Copied GO:0022900 to GO:0055114 with type OBO_REL:is_a
* Deleted GO:0030090 --OBO_REL:is_a--> GO:0009521
* Destroyed object GO:0030090
* Copied GO:0030093 to GO:0044436 with type OBO_REL:is_a
* Copied GO:0030095 to GO:0044436 with type OBO_REL:is_a
* Copied GO:0031976 to GO:0043231 with type OBO_REL:is_a
* Changed synonym scope of GO:0033920 from "Broad" to "Exact"
* Changed name of GO:0034299 from "blastospore formation" to "reproductive blastospore formation"
* Added comment "Note that this term should not be confused with the usage of 'blastospore' to mean any yeast-form fungal cell, as in Candida species."
* Changed definition of GO:0034299 from "The formation of produced from a vegetative mother cell by budding. Blastospores are a type of asexual spore found in some fungi, including Candida species and the class Glomeromycota." to "The formation of a spore following the marked enlargement of part of a cell before separation by a septum. Blastospores are a type of asexual spore found in some fungi, most notably the class Glomeromycota."
* Deleted definition dbxref GOC:ds from GO:0034299
* Deleted definition dbxref ISBN:?? from GO:0034299
* Added definition dbxref GOC:mah to GO:0034299
* Added definition dbxref http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_a_b.shtml#blastospore to GO:0034299
* Added definition dbxref http://bugs.bio.usyd.edu.au/Mycology/Taxonomy/glomeromycota.shtml to GO:0034299
* Copied GO:0042649 to GO:0043231 with type OBO_REL:is_a