ntr/mp: organelle localization

[gocentral]

Hi there,

I have three requests below, 2 ntrs and a parentage issue.

Thanks,

Karen

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1) ntr: centrosome localization

def: The orderly synthesis, assembly, regulation, and motion of structures that place the centrosome in a specific position at a defined time within the cell at large.

parentage: GO:0051179 : localization (see below) GO:0051297 : centrosome organization and biogenesis (?)

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2) ntr: Golgi localization

def: The orderly synthesis, assembly, regulation, and motion of structures that place the Golgi in a specific position at a defined time within the cell at large.

parentage: GO:0051179 : localization (see below) GO:0007030 : Golgi organization and biogenesis (?)

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3) GO:0051179 : localization [only parent is physiological process]

def: The processes by which a substance or cellular entity, such as a protein complex or ORGANELLE, is transported to, and/or maintained in, a specific location.

synonyms: establishment and maintenance of position; establishment and maintenance of substrate location; positioning

Not sure if there should be an additional child of localization, something like 'organelle localization' -- that would probably not be used except as a placeholder.

proposed children:

- GO:0007105 : cytokinesis, site selection def: The process of marking the place where cytokinesis will occur. synonyms: actomyosin ring positioning; contractile ring positioning)

- GO:0031081 : nuclear pore distribution def: The orderly synthesis, assembly, regulation, and motion of structures that place nuclear pores in specific positions within the nuclear envelope at a defined time within the cell at large. synonym: nuclear pore positioning

- GO:0051293 : establishment of spindle localization def: The directed movement of the spindle to a specific location in the cell. synonym: spindle positioning [child of GO:0051234 : establishment of localization?]

- GO:0040001 : establishment of mitotic spindle localization def: The directed movement of the mitotic spindle to a specific location in the cell. [child of GO:0051234 : establishment of localization?]

- GO:0051295 : establishment of meiotic spindle localization def: The directed movement of the meiotic spindle to a specific location in the cell. [child of GO:0051234 : establishment of localization?]

- GO:0048312 : mitochondrion positioning within cell def: Spatial arrangement of mitochondria within the cell.

- GO:0040023 : nuclear positioning def: The orderly synthesis, assembly, regulation, and motion of structures that place the nucleus in a specific position at a defined time within the cell at large.

- GO:0030722 : oocyte nucleus positioning def: The orderly synthesis, assembly, regulation, and motion of structures that place the nucleus in a specific position at a defined time within an oocyte.

- GO:0048126 : oocyte nucleus positioning (sensu Insecta) def: The re-positioning of the oocyte nucleus to a dorsal-anterior position in the egg chamber, an essential step in oocyte dorsal/ventral patterning during oogenesis.

Reported by: kpilcher

Original Ticket: "geneontology/ontology-requests/2864":https://sourceforge.net/p/geneontology/ontology-requests/2864

[gocentral]

Logged In: YES user_id=1056932

P.S. These terms are for PMID: 15800059.

I don't like the terms 'organization and biogenesis' for this gene because it deals with organization but there is no evidence that there is an effect on biogenesis.

Original comment by: kpilcher

[gocentral]

• assigned_to: nobody --> girlwithglasses

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796

I've added the following terms for you: centrosome localization, GO:0051642 (is_a 'organelle localization ; GO: 0051640', is_a 'cell organization and biogenesis ; GO:0016043') Golgi localization, GO:0051645 (is_a 'organelle localization ; GO:0051640', is_a 'cell organization and biogenesis ; GO:0016043')

and am doing a bit of a clean up of all the terms relating to the localization of various cellular entities, including adding the missing paths you mentioned above.

Have added the following terms so far: organelle localization, GO:0051640 cellular localization, GO:0051641 centrosome localization, GO:0051642 ER localization, GO:0051643 plastid localization, GO:0051644 centrosome localization, GO:0051642 Golgi localization, GO:0051645 mitochondrion localization, GO:0051646 nucleus localization, GO:0051647 vesicle localization, GO:0051648 establishment of cellular localization, GO:0051649 establishment of vesicle localization, GO:0051650 maintenance of cellular localization, GO:0051651 maintenance of chromosome localization, GO:0051652 spindle localization, GO:0051653 establishment of mitochondrion localization, GO:0051654 maintenance of vesicle localization, GO:0051655 establishment of organelle localization, GO:0051656 maintenance of organelle localization, GO:0051657 maintenance of nucleus localization, GO:0051658 maintenance of mitochondrion localization, GO:0051659 establishment of centrosome localization, GO:0051660 maintenance of centrosome localization, GO:0051661 oocyte nucleus localization during oocyte axis determination (sensu Insecta), GO:0051662 oocyte nucleus localization during oocyte axis determination, GO:0051663 nuclear pore localization, GO:0051664 lipid raft localization, GO:0051665 actin cortical patch localization, GO:0051666 establishment of plastid localization, GO:0051667 localization within membrane, GO:0051668

and standardized the following term names: GO:0007312: name has changed from 'oocyte nucleus migration' to 'oocyte nucleus migration during oocyte axis determination' GO:0030720: name has changed from 'oocyte positioning' to 'oocyte localization during oogenesis' GO:0030722: name has changed from 'oocyte nucleus positioning' to 'establishment of oocyte nucleus localization during oocyte axis determination' GO:0040023: name has changed from 'nuclear positioning' to 'establishment of nucleus localization' GO:0042070: name has changed from 'oocyte nucleus anchoring' to 'maintenance of oocyte nucleus localization during oocyte axis determination' GO:0045167: name has changed from 'asymmetric protein localization involved in cell fate commitment' to 'asymmetric protein localization during cell fate commitment' GO:0045168: name has changed from 'cell-cell signaling involved in cell fate commitment' to 'cell-cell signaling during cell fate commitment' GO:0048126: name has changed from 'oocyte nucleus positioning (sensu Insecta)' to 'establishment of oocyte nucleus localization during oocyte axis determination (sensu Insecta)' GO:0048127: name has changed from 'oocyte nucleus anchoring (sensu Insecta)' to 'maintenance of oocyte nucleus localization during oocyte axis determination (sensu Insecta)' GO:0048128: name has changed from 'oocyte nucleus migration (sensu Insecta)' to 'oocyte nucleus migration during oocyte axis determination (sensu Insecta)' GO:0048312: name has changed from 'mitochondrion positioning within cell' to 'intracellular distribution of mitochondria'

Am filling in missing relationships as I go along.

Original comment by: girlwithglasses

[gocentral]

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Hi Amelia,

Thanks for doing so much work on this.

I noticed the new term nucleus localization, GO:0051647. We have the term GO:0040023 : nuclear positioning already. I think this might be redundant.

Thanks again,

Karen

Original comment by: kpilcher

[gocentral]

Logged In: YES user_id=473796

Hi Karen,

Can I just check what you want to use your terms for? There are two concepts in localization, the first being moving something to a location, and the second maintaining it in that location, ie:

xxx localization [p] establishment of xxx localization [p] maintenance of xxx localization

Obviously the parent 'xxx localization' covers both concepts. I don't know if you should be using the 'establishment of xxx localization' terms instead...

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=1056932

Hi Amelia,

I only need 'centrosome localization' and 'Golgi localization' for the paper I am annotating (PMID: 15800059).

They create a mutant that (during interphase) has its centrosome dissociated from the nucleus and moves around the cell 3 times faster than controls in a 15-fold larger area. (As a result, the microtubule cytoskeleton is severely disorganized.)

They also show that the Golgi, which is typically juxtaposed to the nucleus, the dispersed about the cell.

Does that answer your question?

Thanks,

Karen

Original comment by: kpilcher

[gocentral]

• status: open --> closed

Original comment by: girlwithglasses

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Logged In: YES user_id=473796

Yup, that's great - thanks Karen.

Have also added establishment of Golgi localization, GO:0051683 maintenance of Golgi localization, GO:0051684 maintenance of ER localization, GO:0051685 establishment of ER localization, GO:0051686 maintenance of spindle localization, GO:0051687 maintenance of plastid localization, GO:0051688

The only one of the terms above which isn't linked to 'localization' is the site selection term - I will have a look at all those site selection terms and see if they can be given more systematic synonyms / names. Closing this item for now, though...

Original comment by: girlwithglasses

[gocentral]

• labels: --> New term request
• milestone: --> TermGenie
• status: closed --> closed-accepted

Original comment by: girlwithglasses