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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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New term 'lumen' for component ontology #1983

Closed gocentral closed 9 years ago

gocentral commented 20 years ago

Suggest that we add a new grouping term 'lumen' to the component ontology (arose from discussions at the August content meeting).

Possible definition:

The volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen or the space between a phospholipid bilayer e.g. nuclear membrane lumen.

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/1989":https://sourceforge.net/p/geneontology/ontology-requests/1989

gocentral commented 20 years ago

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If you have a look in onelook, most of the defs of lumen talk about it being the cavity within a tube or tubular structure (eg. the lumen of a blood vessel). Would this be a case of a special GO meaning for lumen?

Original comment by: girlwithglasses

gocentral commented 20 years ago

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It would indeed. We have 11 'x lumen' terms already in GO, and the definition above is roughly how we use it at the moment...

Original comment by: jl242

gocentral commented 20 years ago

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The trouble is that we have some lumen terms in process which refer to the cavity in a tubular structure (eg. lumen formation, def: Creation of the central hole of a tube through which gases and/or liquids flow.). Don't you think it would be better to find a less ambiguous name? eg. intermembrane space? intra-organelle cavity? Some people may not look at defs when annotating and having a special GO meaning for a commonly used term could cause all manner of misannotations!

Original comment by: girlwithglasses

gocentral commented 20 years ago

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Or maybe just name the term 'organelle lumen'?

Original comment by: girlwithglasses

gocentral commented 19 years ago

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Yes, organelle lumen work work. It could be a child of the new term 'organelle'.

Original comment by: jl242

gocentral commented 19 years ago

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Added new term:

organelle lumen ; GO:0043233

as part_of 'organelle', with appropriate children.

Original comment by: jl242

gocentral commented 19 years ago

Original comment by: jl242