Obsolete term merges

[gocentral]

The following term strings exist both as extant terms and obsolete terms. At the recent consortium meeting, it was suggested that in these cases, the obsolete term should be merged into the extant term, providing there are no annotations. I will do so with these terms unless anyone has any specific objections.

Those terms in full:

shared string: actin cytoskeleton reorganization GO:0007012, name, obsolete GO:0031532, name shared string: actin modification GO:0007013, name, obsolete GO:0030047, name shared string: activin A complex GO:0043509, name GO:0048181, name, obsolete shared string: activin B complex GO:0043510, name GO:0048182, name, obsolete shared string: bent DNA binding GO:0003681, name GO:0006326, name, obsolete shared string: caspase activity GO:0004199, name, obsolete GO:0030693, name shared string: cell surface (sensu Magnoliophyta) GO:0009928, name GO:0009929, name, obsolete shared string: chromatin GO:0000785, name GO:0005717, name, obsolete shared string: chromatin insulator sequence binding GO:0006341, name, obsolete GO:0043035, name shared string: chromosome condensation GO:0000068, name, obsolete GO:0030261, name shared string: clathrin coat GO:0016190, name, obsolete GO:0030118, name shared string: coated vesicle GO:0005909, name, obsolete GO:0030135, name shared string: collagen GO:0005202, name, obsolete GO:0005581, name shared string: condensin complex GO:0000796, name GO:0005676, name, obsolete shared string: condensin core heterodimer GO:0000797, name GO:0008621, name, obsolete shared string: cytokinesis GO:0000910, name GO:0007104, name, obsolete GO:0016288, name, obsolete shared string: delta DNA polymerase complex GO:0005659, name, obsolete GO:0043625, name shared string: double-strand break repair via homologous recombination GO:0000724, name GO:0016924, name, obsolete shared string: immunoglobulin receptor activity GO:0016489, name, obsolete GO:0019763, name shared string: inter-Golgi transport vesicle GO:0005807, name, obsolete GO:0030143, name shared string: juvenile hormone binding GO:0005500, name GO:0006717, name, obsolete shared string: karyogamy GO:0000741, name GO:0007335, name, obsolete shared string: kinetochore GO:0000776, name GO:0005699, name, obsolete shared string: lipid binding GO:0006630, name, obsolete GO:0008289, name shared string: microsporocyte nucleus GO:0043074, name, obsolete GO:0048556, name shared string: nucleosome GO:0000786, name GO:0005718, name, obsolete shared string: periplasmic space GO:0005620, name, obsolete GO:0042597, name shared string: phospholipid scrambling GO:0008498, name, obsolete GO:0017121, name shared string: satellite DNA binding GO:0003696, name GO:0006329, name, obsolete shared string: single-stranded DNA binding GO:0003697, name GO:0006330, name, obsolete shared string: spindle pole GO:0000922, name GO:0030615, name, obsolete shared string: synaptic vesicle endocytosis GO:0008099, name, obsolete GO:0048488, name shared string: synaptic vesicle transport GO:0016181, name, obsolete GO:0048489, name shared string: synaptonemal complex GO:0000795, name GO:0005716, name, obsolete shared string: vesicle fusion GO:0005481, name, obsolete GO:0006906, name shared string: vesicle targeting GO:0005482, name, obsolete GO:0006903, name

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/3320":https://sourceforge.net/p/geneontology/ontology-requests/3320

[gocentral]

Original comment by: mah11

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Logged In: YES user_id=436423

I've attached a file with my witterings on these.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=473796 Originator: YES

The majority of these are OK to merge and so I will do so.

There are still the cases where the two terms were in different ontologies. My feeling is that since the terms are obsolete, and if the obsoletions were long enough ago that the terms are no longer in use, we should just merge them.

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796 Originator: YES

The following are still to be done:

bent DNA binding: GO:0003681, GO:0006326 (obsolete)

chromatin insulator sequence binding: GO:0006341 (obsolete), GO:0043035

collagen: GO:0005202 (obsolete), GO:0005581

juvenile hormone binding: GO:0005500, GO:0006717 (obsolete)

lipid binding: GO:0006630 (obsolete), GO:0008289

phospholipid scrambling: GO:0008498 (obsolete), GO:0017121

satellite DNA binding: GO:0003696, GO:0006329 (obsolete)

single-stranded DNA binding: GO:0003697, GO:0006330 (obsolete)

vesicle fusion: GO:0005481 (obsolete), GO:0006906

vesicle targeting: GO:0005482 (obsolete), GO:0006903

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=735846 Originator: NO

Hi,

I've looked at these terms before and they seem fine to merge:

vesicle fusion: GO:0005481 (obsolete), GO:0006906

vesicle targeting: GO:0005482 (obsolete), GO:0006903

Jen

Original comment by: jenclark

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Logged In: YES user_id=451873 Originator: NO

I agree that in cases where the terms were in different ontologies we should go ahead and merge anyway.

Jane

Original comment by: jl242

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Logged In: YES user_id=631592 Originator: NO

My only worry about merging terms from different ontologies is for groups who have load scripts that check for the integrity of IDs. I don't know if anyone (we don't) would have a load script break because an ID that used to be in function is now a secondary ID in a different ontology.

Biologically, I think it is o.k. to merge all the ones above.

David

Original comment by: ukemi

[gocentral]

• status: open --> closed-fixed

Original comment by: girlwithglasses