[Go-diff] GO update 11/24/2008

[Remote CVS for Gene Ontology]

OBODIFF of gene_ontology_write.obo version 1.324 by 1.326

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0070160
* Created object of type obo:TERM with id GO:0070161
* Populated new object GO:0070160 (macro)
  * Changed name of GO:0070160 from "<new term>" to "occluding junction"
  * Set definition of GO:0070160 to "A cell-cell junction that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other."
  * Added definition dbxref ISBN:0815332181 to GO:0070160
  * Added synonym "occluding cell junction" to GO:0070160
  * Added general dbxref GOC:mah to synonym occluding cell junction of GO:0070160
  * Changed synonym scope of GO:0070160 from "Related" to "Exact"
  * Copied GO:0070160 to GO:0005911 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070160
* Populated new object GO:0070161 (macro)
  * Changed name of GO:0070161 from "<new term>" to "anchoring junction"
  * Set definition of GO:0070161 to "A cell junction that mechanically attaches a cell (and its cytoskeleton) to  neighboring cells or to the extracellular matrix."
  * Added definition dbxref ISBN:0815332181 to GO:0070161
  * Added synonym "anchoring cell junction" to GO:0070161
  * Added general dbxref GOC:mah to synonym anchoring cell junction of GO:0070161
  * Changed synonym scope of GO:0070161 from "Related" to "Exact"
  * Copied GO:0070161 to GO:0030054 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070161
* Changed definition of GO:0005911 from "A specialized region of connection between two cells including but not limited to gap junctions, desmosomes, and tight junctions, but excluding direct cytoplasmic junctions such as ring canals." to "A cell junction that forms a connection between two cells; excludes direct cytoplasmic junctions such as ring canals."
* Added definition dbxref GOC:mah to GO:0005911
* Changed definition of GO:0005912 from "A cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments." to "A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments."
* Added definition dbxref GOC:mah to GO:0005912
* Added definition dbxref http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html to GO:0005912
* Deleted GO:0005912 --OBO_REL:is_a--> GO:0030054
* Copied GO:0005912 to GO:0070161 with type OBO_REL:is_a
* Changed definition of GO:0005915 from "Cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells." to "A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells."
* Added synonym "adhesion belt" to GO:0005915
* Changed synonym scope of GO:0005915 from "Related" to "Exact"
* Changed definition of GO:0005916 from "An electron dense junctional complex, at the end to end contacts of cardiac muscle cells, that contains gap junctions and desmosomes. Most of the disc is formed of a convoluted fascia adherens type of junction into which the actin filaments of the terminal sarcomeres insert (or in the case of muscle cells, myofibrils), desmosomes are also present. The lateral portion of the stepped disc contains gap junctions that couple the cells electrically and thus coordinate the contraction." to "A cell-cell junction that contains the transmembrane protein N-cadherin, which interacts with identical molecules from neighboring cells to form a tight mechanical intercellular link; forms a large portion of the intercalated disc, the structure at which myofibrils terminate in cardiomyocytes."
* Added definition dbxref PMID:11732910 to GO:0005916
* Changed definition of GO:0005918 from "Invertebrate-specific cell-cell junctions which form a band around the apical borders of epithelial cells and attach to actin filaments." to "A cell-cell junction that forms a continuous band around each cell in an epithelium; within the septate junction the membranes of adjacent cells maintain a constant distance of approximately 15 nm; found in invertebrates."
* Deleted definition dbxref ISBN:0815316208 from GO:0005918
* Added definition dbxref ISBN:0815332181 to GO:0005918
* Added definition dbxref PMID:11700298 to GO:0005918
* Deleted GO:0005918 --OBO_REL:is_a--> GO:0005913
* Copied GO:0005918 to GO:0070160 with type OBO_REL:is_a
* Changed definition of GO:0005921 from "Any specialized areas of the plasma membranes of adjacent cells where the membranes are 2-4 nm apart and penetrated by a connexon. This gap junction allows passage of small molecules and electric current. The variety in the properties of gap junctions is reflected in the number of connexins, the family of proteins which form the junction." to "A cell-cell junction that is composed of an array of small channels that permit small molecules to pass from one cell to another. At gap junctions, the membranes of two adjacent cells are separated by a uniform narrow gap of about 2?4 nm that is spanned by channel-forming proteins called connexins, which form hexagonal tubes called connexons."
* Deleted definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) from GO:0005921
* Added definition dbxref GOC:mah to GO:0005921
* Added definition dbxref http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_g.html to GO:0005921
* Added definition dbxref ISBN:0815332181 to GO:0005921
* Deleted GO:0005921 --part_of--> GO:0014704
* Changed definition of GO:0005923 from "A belt-like region of very close contact between the plasma membranes of adjacent cells so that the intercellular space is completely occluded. They occur in epithelia and brain endothelia." to "An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes."
* Deleted definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) from GO:0005923
* Added definition dbxref GOC:mah to GO:0005923
* Added definition dbxref ISBN:0815332181 to GO:0005923
* Deleted GO:0005923 --OBO_REL:is_a--> GO:0005911
* Copied GO:0005923 to GO:0070160 with type OBO_REL:is_a
* Changed synonym scope of GO:0005925 from "Exact" to "Related"
* Added general dbxref GOC:tb to synonym UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase-4-reductase activity of GO:0010280
* Changed synonym scope of GO:0010280 from "Exact" to "Narrow"
* Changed definition of GO:0014704 from "Specialised type of cell-cell junction in cardiac muscle, which mediates mechanical and electrochemical integration between the individual cardiomyocytes. Consist of three different kinds of substructures: adherens junctions, desmosomes and gap junctions." to "A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells."
* Added definition dbxref PMID:11732910 to GO:0014704
* Deleted GO:0014704 --OBO_REL:is_a--> GO:0030054
* Copied GO:0014704 to GO:0005911 with type OBO_REL:is_a
* Changed definition of GO:0030054 from "A specialized region of connection between two cells or between a cell and the extracellular matrix." to "A plasma membrane part that forms a specialized region of connection between two cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix."
* Added definition dbxref GOC:mah to GO:0030054
* Added definition dbxref http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html to GO:0030054
* Changed definition of GO:0030055 from "A specialized region of connection between a cell and the extracellular matrix." to "A cell junction that forms a connection between a cell and the extracellular matrix."
* Added definition dbxref GOC:mah to GO:0030055
* Added synonym "hemi-adherens junction" to GO:0030056
* Added general dbxref http://www.wormatlas.org/glossaries/hglossary.htm#hemiadherensjunction to synonym hemi-adherens junction of GO:0030056
* Changed definition of GO:0030057 from "A specialised type of cell junction into which intermediate filaments of adjacent cells are inserted. This type of cell junction is characteristic of epithelia. Desmosomes are particularly conspicuous in tissues such as skin that have to withstand mechanical stress." to "A cell-cell junction in which: on the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular anchor proteins; a bundle of keratin intermediate filaments is attached to the surface of each plaque; transmembrane adhesion proteins of the cadherin family bind to the plaques and interact through their extracellular domains to hold the adjacent membranes together by a Ca2+-dependent mechanism."
* Deleted definition dbxref ISBN:0815316208 from GO:0030057
* Added definition dbxref GOC:mah to GO:0030057
* Added definition dbxref ISBN:0815332181 to GO:0030057
* Deleted GO:0030057 --part_of--> GO:0014704
* Copied GO:0030057 to GO:0070161 with type OBO_REL:is_a
* Changed definition of GO:0033010 from "A highly specialized junction found in vertebrates, which forms between a neuron and a glial cell, and has structural similarity to Drosophila septate junctions. It flanks the node of Ranvier in myelinated nerve and electrically isolates the myelinated from unmyelinated nerve segments and physically separates the voltage-gated sodium channels at the node from the cluster of potassium channels underneath the myelin sheath." to "A highly specialized cell-cell junction found in vertebrates, which forms between a neuron and a glial cell, and has structural similarity to Drosophila septate junctions. It flanks the node of Ranvier in myelinated nerve and electrically isolates the myelinated from unmyelinated nerve segments and physically separates the voltage-gated sodium channels at the node from the cluster of potassium channels underneath the myelin sheath."
* Added synonym "apical cell junction complex" to GO:0043296
* Added general dbxref GOC:mah to synonym apical cell junction complex of GO:0043296
* Changed synonym scope of GO:0043296 from "Related" to "Exact"
* Deleted general dbxref GOC:tb from synonym oocyte nucleus localization during oocyte axis determination of GO:0051663
* Deleted general dbxref GOC:dph from synonym oocyte nucleus localization during oocyte axis determination of GO:0051663
* Changed synonym scope of GO:0051663 from "Related" to "Exact"