XP:biological process xp sequence molecule

This page describes the (ongoing, nascent) work on defining certain BP terms using SO cross-products

Methodology

Obol was used to generate the initial version of the file. This was then vetted by cjm

The current version has many false negatives (ie BP terms that could be defined using SO) since there are many terms obol cannot parse. These can be added later either manually or through refinements to Obol

How to get it

• go/scratch/xps/

OBO-Edit users: point OE at the -imports.obo file.

or just browse

CHEBI/SO overlaps

Bases and amino acids

• inosine

etc

Peptide

• peptide (SO has active_peptide as an EXACT synonym. mistake?)

SO/CC overlaps

Centromere

• SO:0000577 centromere [DEF: "A region of chromosome where the spindle fibers attach during mitosis and meiosis."]
• GO:0005698 centromere [DEF: "OBSOLETE. The region of a eukaryotic chromosome that is attached to the spindle during nuclear division. It is defined genetically as the region of the chromosome that always segregates at the first division of meiosis; the region of the chromosome in which no crossing over occurs. At the start of M phase, each chromosome consists of two sister chromatids with a constriction at a point which forms the centromere. During late prophase two kinetochores assemble on each centromere, one kinetochore on each sister chromatid."]
• GO:0000775 chromosome, pericentric region [DEF: "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."] comment: This term was made obsolete because it is genetically defined region and not a specific subcellular localization.

GO has the following:

GO:0030702 chromatin silencing at centromere 
GO:0031055 chromatin remodeling at centromere 
GO:0031059 histone deacetylation at centromere 
GO:0031066 regulation of histone deacetylation at centromere 
GO:0031067 negative regulation of histone deacetylation at centromere 
GO:0031068 positive regulation of histone deacetylation at centromere 
GO:0034080 DNA replication-independent nucleosome assembly at centromere 
GO:0043505 centromere-specific nucleosome 
GO:0051756 meiotic sister chromatid centromere separation

Telomere

Similar comments apply

Here there are two GO terms to choose from:

• GO:0000781 chromosome, telomeric region (related synonym: telomere)
• GO:0000782 telomere cap complex

The former is what is usually meant in terms with the string "telomere" or "telomeric"

Chromosome

Both SO and CC have chromosome

• SO:0000340 chromosome [DEF: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication."]
• GO:0005694 chromosome [DEF: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information."]

terms such as

  GO:0050000 ! chromosome localization

are defined in XP:biological_process_xp_cellular_component